{ "code": 200, "status": "SUCCESS", "message": "Experiment page", "data": { "dataType": "SC_RNA_SEQ", "columnDescriptions": [ { "title": "Library ID", "infoBubble": "Identifier of the RNA-Seq library", "attributes": [ "result.library.id" ], "columnType": "STRING", "export": true }, { "title": "Cell type ID", "infoBubble": "ID of the cell type of the sample", "attributes": [ "result.annotation.rawDataCondition.cellType.id" ], "columnType": "ANAT_ENTITY", "export": true }, { "title": "Cell type name", "infoBubble": "Name of the cell type of the sample", "attributes": [ "result.annotation.rawDataCondition.cellType.name" ], "columnType": "STRING", "export": true }, { "title": "Cell type author annotation", "infoBubble": "Free text annotation of cell type as provided by authors", "attributes": [ "result.annotation.rawDataCondition.cellTypeAuthorAnnotation" ], "columnType": "STRING", "export": true }, { "title": "Anat. entity ID", "infoBubble": "ID of the anatomical localization of the sample", "attributes": [ "result.annotation.rawDataCondition.anatEntity.id" ], "columnType": "ANAT_ENTITY", "export": true }, { "title": "Anat. entity name", "infoBubble": "Name of the anatomical localization of the sample", "attributes": [ "result.annotation.rawDataCondition.anatEntity.name" ], "columnType": "STRING", "export": true }, { "title": "Anat. entity author annotation", "infoBubble": "Free text annotation of anatomical localization of the sample as provided by authors", "attributes": [ "result.annotation.rawDataCondition.anatEntityAuthorAnnotation" ], "columnType": "STRING", "export": true }, { "title": "Stage ID", "infoBubble": "ID of the developmental and life stage of the sample", "attributes": [ "result.annotation.rawDataCondition.devStage.id" ], "columnType": "DEV_STAGE", "export": true }, { "title": "Stage name", "infoBubble": "Name of the developmental and life stage of the sample", "attributes": [ "result.annotation.rawDataCondition.devStage.name" ], "columnType": "STRING", "export": true }, { "title": "Stage author annotation", "infoBubble": "Free text annotation of the developmental and life stage of the sample as provided by authors", "attributes": [ "result.annotation.rawDataCondition.devStageAuthorAnnotation" ], "columnType": "STRING", "export": true }, { "title": "Sex", "infoBubble": "Annotation of the sex of the sample", "attributes": [ "result.annotation.rawDataCondition.sex" ], "columnType": "STRING", "export": true }, { "title": "Strain", "infoBubble": "Annotation of the strain of the sample", "attributes": [ "result.annotation.rawDataCondition.strain" ], "columnType": "STRING", "export": true }, { "title": "Time", "infoBubble": "Free text annotation of the time of sampling as provided by authors", "attributes": [ "result.annotation.rawDataCondition.time" ], "columnType": "STRING", "export": true }, { "title": "Time unit", "infoBubble": "Unit for the time of sampling as provided by authors", "attributes": [ "result.annotation.rawDataCondition.timeUnit" ], "columnType": "STRING", "export": true }, { "title": "Species", "attributes": [ "result.annotation.rawDataCondition.species.genus", "result.annotation.rawDataCondition.species.speciesName" ], "columnType": "STRING", "export": true }, { "title": "Physiological status", "infoBubble": "Physiological status of the organism at time of sampling", "attributes": [ "result.annotation.physiologicalStatus" ], "columnType": "STRING", "export": true }, { "title": "Technology", "attributes": [ "result.library.technology.protocolName" ], "columnType": "STRING", "export": true }, { "title": "Sequencing platform", "attributes": [ "result.library.technology.sequencingPlatfomName" ], "columnType": "STRING", "export": true }, { "title": "Sequenced transcript part", "infoBubble": "Possible values are: full length, all parts of the transcript are sequenced; 3': only the 3' end of the transcript is sequenced; 5': only the 5' end of the transcript is sequenced.", "attributes": [ "result.library.technology.sequencedTranscriptPart" ], "columnType": "STRING", "export": true }, { "title": "Fractionation", "infoBubble": "Possible values are: cell, transcripts are extracted from the cell; nuclei, transcripts are extracted from the nucleus.", "attributes": [ "result.library.technology.cellCompartment" ], "columnType": "STRING", "export": true }, { "title": "Fragmentation", "infoBubble": "Size of the RNA fragmentation", "attributes": [ "result.library.technology.fragmentation" ], "columnType": "NUMERIC", "export": true }, { "title": "Run sequencing type", "infoBubble": "Paired-end or single-read run", "attributes": [ "result.library.technology.libraryType" ], "columnType": "STRING", "export": true }, { "title": "Total read count", "infoBubble": "Total number of reads for the library.", "attributes": [ "result.library.pipelineSummary.allReadsCount" ], "columnType": "NUMERIC", "export": true }, { "title": "Mapped read count", "infoBubble": "Number of reads that could be mapped to the transcriptome.", "attributes": [ "result.library.pipelineSummary.mappedReadsCount" ], "columnType": "NUMERIC", "export": true }, { "title": "Total UMI count", "infoBubble": "Total number of individual RNA molecules (UMI) for the annotated sample. Only applicable for libraries producing UMIs.", "attributes": [ "result.pipelineSummary.allUMIsCount" ], "columnType": "NUMERIC", "export": true }, { "title": "Mapped UMI count", "infoBubble": "Number of UMIs that could be mapped to the transcriptome. Only applicable for libraries producing UMIs.", "attributes": [ "result.pipelineSummary.mappedUMIsCount" ], "columnType": "NUMERIC", "export": true }, { "title": "Distinct rank count", "infoBubble": "When performing a fractional ranking of the genes in the annotated sample, based on their expression level, number of distinct ranks observed, to have a value of the power for distinguishing expression levels. Used as a weight to compute a weighted mean rank accross samples for each gene and compute expression scores in Bgee.", "attributes": [ "result.pipelineSummary.distinctRankCount" ], "columnType": "NUMERIC", "export": true }, { "title": "Max rank", "infoBubble": "When performing a fractional ranking of the genes in the annotated sample, based on their expression level, maximum rank attained in the sample. Used to normalize ranks accross samples and compute expression scores in Bgee.", "attributes": [ "result.pipelineSummary.maxRank" ], "columnType": "NUMERIC", "export": true }, { "title": "Link to processed expression values", "infoBubble": "See the processed expression value results for this assay", "columnType": "LINK_TO_PROC_EXPR_VALUES", "filterTargets": [ { "valueAttributeName": "result.library.experiment.id", "urlParameterName": "filter_exp_id" }, { "valueAttributeName": "result.library.id", "urlParameterName": "filter_assay_id" }, { "valueAttributeName": "result.annotation.rawDataCondition.cellType.id", "urlParameterName": "filter_cell_type_id" }, { "valueAttributeName": "result.annotation.rawDataCondition.anatEntity.id", "urlParameterName": "filter_anat_entity_id" }, { "valueAttributeName": "result.annotation.rawDataCondition.devStage.id", "urlParameterName": "filter_stage_id" }, { "valueAttributeName": "result.annotation.rawDataCondition.sex", "urlParameterName": "filter_sex" }, { "valueAttributeName": "result.annotation.rawDataCondition.strain", "urlParameterName": "filter_strain" }, { "valueAttributeName": "result.annotation.rawDataCondition.species.id", "urlParameterName": "filter_species_id" } ], "export": false } ], "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "assays": [ { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 152617845, "mappedReadsCount": 89953327, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138748" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0002063", "name": "type II pneumocyte" }, "cellTypeAuthorAnnotation": "AT2, Epithelia", "devStage": { "id": "HsapDv:0000123", "name": "29-year-old stage (human)" }, "devStageAuthorAnnotation": "25-30 (29 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 5.262325, "sdRefIntergenicDistribution": 2.126089, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 337077, "distinctRankCount": 990, "maxRank": 23459.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 152617845, "mappedReadsCount": 89953327, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138748" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000583", "name": "alveolar macrophage" }, "cellTypeAuthorAnnotation": "Macro_alveolar, Immune", "devStage": { "id": "HsapDv:0000123", "name": "29-year-old stage (human)" }, "devStageAuthorAnnotation": "25-30 (29 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 67.735375, "sdRefIntergenicDistribution": 1.367573, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 16369, "distinctRankCount": 153, "maxRank": 19015.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 152617845, "mappedReadsCount": 89953327, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138748" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000192", "name": "smooth muscle cell" }, "cellTypeAuthorAnnotation": "Muscle_smooth_pulmonary, Stroma", "devStage": { "id": "HsapDv:0000123", "name": "29-year-old stage (human)" }, "devStageAuthorAnnotation": "25-30 (29 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 150.992174, "sdRefIntergenicDistribution": 1.310016, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 6880, "distinctRankCount": 77, "maxRank": 18410.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 152617845, "mappedReadsCount": 89953327, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138748" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:1001603", "name": "lung macrophage" }, "cellTypeAuthorAnnotation": "Macro_CHIT1, Immune", "devStage": { "id": "HsapDv:0000123", "name": "29-year-old stage (human)" }, "devStageAuthorAnnotation": "25-30 (29 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 827.355652, "sdRefIntergenicDistribution": 1.371065, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1289, "distinctRankCount": 25, "maxRank": 17852.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 152617845, "mappedReadsCount": 89953327, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138748" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:1001603", "name": "lung macrophage" }, "cellTypeAuthorAnnotation": "Macro_intravascular, Immune", "devStage": { "id": "HsapDv:0000123", "name": "29-year-old stage (human)" }, "devStageAuthorAnnotation": "25-30 (29 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 430.098128, "sdRefIntergenicDistribution": 1.233569, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 2354, "distinctRankCount": 37, "maxRank": 17968.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 152617845, "mappedReadsCount": 89953327, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138748" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:1001568", "name": "pulmonary artery endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_arterial_pulmonary, Vascular", "devStage": { "id": "HsapDv:0000123", "name": "29-year-old stage (human)" }, "devStageAuthorAnnotation": "25-30 (29 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 166.654486, "sdRefIntergenicDistribution": 1.315975, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 6049, "distinctRankCount": 61, "maxRank": 18482.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 152617845, "mappedReadsCount": 89953327, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138748" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0002543", "name": "vein endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_venous_pulmonary, Vascular", "devStage": { "id": "HsapDv:0000123", "name": "29-year-old stage (human)" }, "devStageAuthorAnnotation": "25-30 (29 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 60.301395, "sdRefIntergenicDistribution": 1.406563, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 18007, "distinctRankCount": 154, "maxRank": 19155.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 152617845, "mappedReadsCount": 89953327, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138748" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0002543", "name": "vein endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_venous_systemic, Vascular", "devStage": { "id": "HsapDv:0000123", "name": "29-year-old stage (human)" }, "devStageAuthorAnnotation": "25-30 (29 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 167.074239, "sdRefIntergenicDistribution": 1.393820, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 6511, "distinctRankCount": 74, "maxRank": 18337.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 152617845, "mappedReadsCount": 89953327, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138748" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0002553", "name": "fibroblast of lung" }, "cellTypeAuthorAnnotation": "Fibro_adventitial, Stroma", "devStage": { "id": "HsapDv:0000123", "name": "29-year-old stage (human)" }, "devStageAuthorAnnotation": "25-30 (29 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 6.742830, "sdRefIntergenicDistribution": 1.708201, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 196126, "distinctRankCount": 738, "maxRank": 22174.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 152617845, "mappedReadsCount": 89953327, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138748" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0002553", "name": "fibroblast of lung" }, "cellTypeAuthorAnnotation": "Fibro_alveolar, Stroma", "devStage": { "id": "HsapDv:0000123", "name": "29-year-old stage (human)" }, "devStageAuthorAnnotation": "25-30 (29 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 95.395121, "sdRefIntergenicDistribution": 1.367438, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 10743, "distinctRankCount": 104, "maxRank": 18985.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 152617845, "mappedReadsCount": 89953327, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138748" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0002553", "name": "fibroblast of lung" }, "cellTypeAuthorAnnotation": "Fibro_immune_recruiting, Stroma", "devStage": { "id": "HsapDv:0000123", "name": "29-year-old stage (human)" }, "devStageAuthorAnnotation": "25-30 (29 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 102.190428, "sdRefIntergenicDistribution": 1.514450, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 11264, "distinctRankCount": 130, "maxRank": 18726.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 152617845, "mappedReadsCount": 89953327, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138748" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000623", "name": "natural killer cell" }, "cellTypeAuthorAnnotation": "NK_CD16hi, Immune", "devStage": { "id": "HsapDv:0000123", "name": "29-year-old stage (human)" }, "devStageAuthorAnnotation": "25-30 (29 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 173.547812, "sdRefIntergenicDistribution": 1.318497, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 5849, "distinctRankCount": 65, "maxRank": 18422.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 152617845, "mappedReadsCount": 89953327, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138748" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000160", "name": "goblet cell" }, "cellTypeAuthorAnnotation": "Secretory_Goblet, Epithelia", "devStage": { "id": "HsapDv:0000123", "name": "29-year-old stage (human)" }, "devStageAuthorAnnotation": "25-30 (29 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 1255.546748, "sdRefIntergenicDistribution": 1.322236, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 818, "distinctRankCount": 21, "maxRank": 17769.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 152617845, "mappedReadsCount": 89953327, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138748" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000158", "name": "club cell" }, "cellTypeAuthorAnnotation": "Secretory_Club, Epithelia", "devStage": { "id": "HsapDv:0000123", "name": "29-year-old stage (human)" }, "devStageAuthorAnnotation": "25-30 (29 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 380.394486, "sdRefIntergenicDistribution": 1.406983, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 2325, "distinctRankCount": 34, "maxRank": 17938.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 152617845, "mappedReadsCount": 89953327, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138748" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000897", "name": "CD4-positive, alpha-beta memory T cell" }, "cellTypeAuthorAnnotation": "CD4_TRM, Immune", "devStage": { "id": "HsapDv:0000123", "name": "29-year-old stage (human)" }, "devStageAuthorAnnotation": "25-30 (29 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 734.824204, "sdRefIntergenicDistribution": 1.463717, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1263, "distinctRankCount": 20, "maxRank": 17803.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 152617845, "mappedReadsCount": 89953327, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138748" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000990", "name": "conventional dendritic cell" }, "cellTypeAuthorAnnotation": "DC_2, Immune", "devStage": { "id": "HsapDv:0000123", "name": "29-year-old stage (human)" }, "devStageAuthorAnnotation": "25-30 (29 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 194.299039, "sdRefIntergenicDistribution": 1.500829, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 5784, "distinctRankCount": 75, "maxRank": 18248.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 152617845, "mappedReadsCount": 89953327, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138748" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000067", "name": "ciliated epithelial cell" }, "cellTypeAuthorAnnotation": "Ciliated, Epithelia", "devStage": { "id": "HsapDv:0000123", "name": "29-year-old stage (human)" }, "devStageAuthorAnnotation": "25-30 (29 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 18.746061, "sdRefIntergenicDistribution": 1.640970, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 63259, "distinctRankCount": 451, "maxRank": 21440.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 152617845, "mappedReadsCount": 89953327, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138748" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0002144", "name": "capillary endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_Cap_g, Vascular", "devStage": { "id": "HsapDv:0000123", "name": "29-year-old stage (human)" }, "devStageAuthorAnnotation": "25-30 (29 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 93.378797, "sdRefIntergenicDistribution": 1.372528, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 11431, "distinctRankCount": 109, "maxRank": 18795.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 152617845, "mappedReadsCount": 89953327, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138748" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0009115", "name": "lymph node lymphatic vessel endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_Lymphatic, Vascular", "devStage": { "id": "HsapDv:0000123", "name": "29-year-old stage (human)" }, "devStageAuthorAnnotation": "25-30 (29 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 11.818097, "sdRefIntergenicDistribution": 1.523520, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 99354, "distinctRankCount": 550, "maxRank": 21567.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 152617845, "mappedReadsCount": 89953327, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138748" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:1000413", "name": "endothelial cell of artery" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_arterial_systemic, Vascular", "devStage": { "id": "HsapDv:0000123", "name": "29-year-old stage (human)" }, "devStageAuthorAnnotation": "25-30 (29 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 1123.454399, "sdRefIntergenicDistribution": 1.253099, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 876, "distinctRankCount": 22, "maxRank": 17742.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 152617845, "mappedReadsCount": 89953327, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138748" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0002062", "name": "type I pneumocyte" }, "cellTypeAuthorAnnotation": "AT1 , Epithelia", "devStage": { "id": "HsapDv:0000123", "name": "29-year-old stage (human)" }, "devStageAuthorAnnotation": "25-30 (29 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 12.415569, "sdRefIntergenicDistribution": 1.658725, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 98631, "distinctRankCount": 483, "maxRank": 21765.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 152617845, "mappedReadsCount": 89953327, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138748" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000186", "name": "myofibroblast cell" }, "cellTypeAuthorAnnotation": "Fibro_myofibroblast, Stroma", "devStage": { "id": "HsapDv:0000123", "name": "29-year-old stage (human)" }, "devStageAuthorAnnotation": "25-30 (29 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 290.800882, "sdRefIntergenicDistribution": 1.285003, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 3333, "distinctRankCount": 43, "maxRank": 18135.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 171499603, "mappedReadsCount": 108600695, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138751" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0002144", "name": "capillary endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_Cap_a, Vascular", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 3.215925, "sdRefIntergenicDistribution": 2.191935, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 649105, "distinctRankCount": 929, "maxRank": 24335.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 171499603, "mappedReadsCount": 108600695, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138751" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0002144", "name": "capillary endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_Cap_g, Vascular", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 2.488541, "sdRefIntergenicDistribution": 2.581527, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1298314, "distinctRankCount": 1460, "maxRank": 25215.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 171499603, "mappedReadsCount": 108600695, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138751" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000583", "name": "alveolar macrophage" }, "cellTypeAuthorAnnotation": "Macro_alveolar, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 2.407190, "sdRefIntergenicDistribution": 2.011391, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 722840, "distinctRankCount": 1335, "maxRank": 23975.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 171499603, "mappedReadsCount": 108600695, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138751" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0002062", "name": "type I pneumocyte" }, "cellTypeAuthorAnnotation": "AT1 , Epithelia", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 13.648137, "sdRefIntergenicDistribution": 1.561802, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 86003, "distinctRankCount": 362, "maxRank": 22056.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 171499603, "mappedReadsCount": 108600695, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138751" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000814", "name": "mature NK T cell" }, "cellTypeAuthorAnnotation": "NKT, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 6.428026, "sdRefIntergenicDistribution": 1.745544, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 211728, "distinctRankCount": 513, "maxRank": 22649.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 171499603, "mappedReadsCount": 108600695, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138751" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:1001568", "name": "pulmonary artery endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_arterial_pulmonary, Vascular", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 3.201910, "sdRefIntergenicDistribution": 2.053307, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 563028, "distinctRankCount": 986, "maxRank": 24319.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 171499603, "mappedReadsCount": 108600695, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138751" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0009089", "name": "lung pericyte" }, "cellTypeAuthorAnnotation": "Muscle_pericyte_pulmonary, Stroma", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 32.060664, "sdRefIntergenicDistribution": 1.382206, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 33354, "distinctRankCount": 183, "maxRank": 20560.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 171499603, "mappedReadsCount": 108600695, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138751" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000798", "name": "gamma-delta T cell" }, "cellTypeAuthorAnnotation": "gdT, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 15.154365, "sdRefIntergenicDistribution": 1.598224, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 78027, "distinctRankCount": 334, "maxRank": 21547.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 171499603, "mappedReadsCount": 108600695, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138751" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000990", "name": "conventional dendritic cell" }, "cellTypeAuthorAnnotation": "DC_1, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 28.969000, "sdRefIntergenicDistribution": 1.447307, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 38083, "distinctRankCount": 269, "maxRank": 20017.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 171499603, "mappedReadsCount": 108600695, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138751" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000990", "name": "conventional dendritic cell" }, "cellTypeAuthorAnnotation": "DC_2, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 24.084540, "sdRefIntergenicDistribution": 1.441486, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 45679, "distinctRankCount": 279, "maxRank": 20500.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 171499603, "mappedReadsCount": 108600695, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138751" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000990", "name": "conventional dendritic cell" }, "cellTypeAuthorAnnotation": "DC_activated, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 228.010131, "sdRefIntergenicDistribution": 1.407623, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 4516, "distinctRankCount": 58, "maxRank": 18306.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 171499603, "mappedReadsCount": 108600695, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138751" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0002543", "name": "vein endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_venous_pulmonary, Vascular", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 21.026599, "sdRefIntergenicDistribution": 1.406571, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 51901, "distinctRankCount": 261, "maxRank": 20899.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 171499603, "mappedReadsCount": 108600695, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138751" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0002543", "name": "vein endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_venous_systemic, Vascular", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 34.840052, "sdRefIntergenicDistribution": 1.421367, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 31606, "distinctRankCount": 224, "maxRank": 20023.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 171499603, "mappedReadsCount": 108600695, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138751" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000624", "name": "CD4-positive, alpha-beta T cell" }, "cellTypeAuthorAnnotation": "CD4_EM/Effector, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 18.688776, "sdRefIntergenicDistribution": 1.532042, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 61005, "distinctRankCount": 302, "maxRank": 21084.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 171499603, "mappedReadsCount": 108600695, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138751" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000624", "name": "CD4-positive, alpha-beta T cell" }, "cellTypeAuthorAnnotation": "CD4_naive/CM, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 109.724875, "sdRefIntergenicDistribution": 1.301304, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 8915, "distinctRankCount": 94, "maxRank": 18797.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 171499603, "mappedReadsCount": 108600695, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138751" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000057", "name": "fibroblast" }, "cellTypeAuthorAnnotation": "NAF_perineurial, Stroma", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 764.363947, "sdRefIntergenicDistribution": 1.219163, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1132, "distinctRankCount": 21, "maxRank": 17859.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 171499603, "mappedReadsCount": 108600695, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138751" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0002553", "name": "fibroblast of lung" }, "cellTypeAuthorAnnotation": "Fibro_adventitial, Stroma", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 5.960399, "sdRefIntergenicDistribution": 1.645254, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 218382, "distinctRankCount": 577, "maxRank": 23196.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 171499603, "mappedReadsCount": 108600695, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138751" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0002553", "name": "fibroblast of lung" }, "cellTypeAuthorAnnotation": "Fibro_alveolar, Stroma", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 9.462892, "sdRefIntergenicDistribution": 1.468537, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 122963, "distinctRankCount": 417, "maxRank": 22142.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 171499603, "mappedReadsCount": 108600695, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138751" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000192", "name": "smooth muscle cell" }, "cellTypeAuthorAnnotation": "Muscle_smooth_pulmonary, Stroma", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 15.259356, "sdRefIntergenicDistribution": 1.415749, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 73488, "distinctRankCount": 284, "maxRank": 21300.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 171499603, "mappedReadsCount": 108600695, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138751" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000913", "name": "effector memory CD8-positive, alpha-beta T cell" }, "cellTypeAuthorAnnotation": "CD8_EM, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 64.701743, "sdRefIntergenicDistribution": 1.368511, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 15575, "distinctRankCount": 141, "maxRank": 19299.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 171499603, "mappedReadsCount": 108600695, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138751" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000913", "name": "effector memory CD8-positive, alpha-beta T cell" }, "cellTypeAuthorAnnotation": "CD8_EM/EMRA, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 5.717837, "sdRefIntergenicDistribution": 1.805834, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 248098, "distinctRankCount": 549, "maxRank": 22828.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 171499603, "mappedReadsCount": 108600695, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138751" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0002633", "name": "respiratory basal cell" }, "cellTypeAuthorAnnotation": "Basal, Epithelia", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 35.207540, "sdRefIntergenicDistribution": 1.401916, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 30293, "distinctRankCount": 223, "maxRank": 20206.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 171499603, "mappedReadsCount": 108600695, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138751" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0001054", "name": "CD14-positive monocyte" }, "cellTypeAuthorAnnotation": "Monocyte_CD14, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 56.014193, "sdRefIntergenicDistribution": 1.401886, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 19569, "distinctRankCount": 159, "maxRank": 19286.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 171499603, "mappedReadsCount": 108600695, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138751" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000909", "name": "CD8-positive, alpha-beta memory T cell" }, "cellTypeAuthorAnnotation": "CD8_TRM, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 212.689746, "sdRefIntergenicDistribution": 1.312765, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 4597, "distinctRankCount": 60, "maxRank": 18414.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 171499603, "mappedReadsCount": 108600695, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138751" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000909", "name": "CD8-positive, alpha-beta memory T cell" }, "cellTypeAuthorAnnotation": "CD8_TRM/EM, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 40.587296, "sdRefIntergenicDistribution": 1.414544, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 25991, "distinctRankCount": 183, "maxRank": 19900.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 171499603, "mappedReadsCount": 108600695, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138751" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0002396", "name": "CD14-low, CD16-positive monocyte" }, "cellTypeAuthorAnnotation": "Monocyte_CD16, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 22.627883, "sdRefIntergenicDistribution": 1.405042, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 48167, "distinctRankCount": 259, "maxRank": 20427.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 171499603, "mappedReadsCount": 108600695, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138751" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000186", "name": "myofibroblast cell" }, "cellTypeAuthorAnnotation": "Fibro_myofibroblast, Stroma", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 128.540979, "sdRefIntergenicDistribution": 1.287857, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 7767, "distinctRankCount": 73, "maxRank": 18788.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 171499603, "mappedReadsCount": 108600695, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138751" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000235", "name": "macrophage" }, "cellTypeAuthorAnnotation": "Macro_AW_CX3CR1, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 599.872217, "sdRefIntergenicDistribution": 1.215352, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1766, "distinctRankCount": 28, "maxRank": 17860.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 171499603, "mappedReadsCount": 108600695, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138751" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000623", "name": "natural killer cell" }, "cellTypeAuthorAnnotation": "NK_CD11d, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 264.689637, "sdRefIntergenicDistribution": 1.280990, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 3618, "distinctRankCount": 50, "maxRank": 18247.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 171499603, "mappedReadsCount": 108600695, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138751" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000623", "name": "natural killer cell" }, "cellTypeAuthorAnnotation": "NK_CD16hi, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 16.320863, "sdRefIntergenicDistribution": 1.541548, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 70870, "distinctRankCount": 342, "maxRank": 21458.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 171499603, "mappedReadsCount": 108600695, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138751" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000623", "name": "natural killer cell" }, "cellTypeAuthorAnnotation": "NK_CD56bright, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 156.861440, "sdRefIntergenicDistribution": 1.289153, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 6304, "distinctRankCount": 83, "maxRank": 18562.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 171499603, "mappedReadsCount": 108600695, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138751" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:1001603", "name": "lung macrophage" }, "cellTypeAuthorAnnotation": "Macro_CHIT1, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 23.498244, "sdRefIntergenicDistribution": 1.433783, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 48147, "distinctRankCount": 274, "maxRank": 20517.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 171499603, "mappedReadsCount": 108600695, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138751" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:1001603", "name": "lung macrophage" }, "cellTypeAuthorAnnotation": "Macro_dividing, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 27.873305, "sdRefIntergenicDistribution": 1.487645, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 41551, "distinctRankCount": 291, "maxRank": 20501.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 171499603, "mappedReadsCount": 108600695, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138751" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:1001603", "name": "lung macrophage" }, "cellTypeAuthorAnnotation": "Macro_intermediate, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 630.936514, "sdRefIntergenicDistribution": 1.384686, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1470, "distinctRankCount": 22, "maxRank": 17933.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 171499603, "mappedReadsCount": 108600695, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138751" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:1001603", "name": "lung macrophage" }, "cellTypeAuthorAnnotation": "Macro_interstitial, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 44.348358, "sdRefIntergenicDistribution": 1.399504, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 25268, "distinctRankCount": 167, "maxRank": 19365.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 171499603, "mappedReadsCount": 108600695, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138751" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:1001603", "name": "lung macrophage" }, "cellTypeAuthorAnnotation": "Macro_intravascular, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 7.017128, "sdRefIntergenicDistribution": 1.696799, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 186220, "distinctRankCount": 555, "maxRank": 22794.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 171499603, "mappedReadsCount": 108600695, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138751" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000897", "name": "CD4-positive, alpha-beta memory T cell" }, "cellTypeAuthorAnnotation": "CD4_TRM, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 35.266987, "sdRefIntergenicDistribution": 1.382147, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 29620, "distinctRankCount": 218, "maxRank": 20104.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 171499603, "mappedReadsCount": 108600695, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138751" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000077", "name": "mesothelial cell" }, "cellTypeAuthorAnnotation": "Mesothelia, Stroma", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 500.281288, "sdRefIntergenicDistribution": 1.182118, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1720, "distinctRankCount": 23, "maxRank": 17979.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 171499603, "mappedReadsCount": 108600695, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138751" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000097", "name": "mast cell" }, "cellTypeAuthorAnnotation": "Mast_cell , Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 223.892268, "sdRefIntergenicDistribution": 1.259960, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 4125, "distinctRankCount": 46, "maxRank": 18265.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 171499603, "mappedReadsCount": 108600695, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138751" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:1000413", "name": "endothelial cell of artery" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_arterial_systemic, Vascular", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 61.118367, "sdRefIntergenicDistribution": 1.311080, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 16690, "distinctRankCount": 127, "maxRank": 19528.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 171499603, "mappedReadsCount": 108600695, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138751" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000940", "name": "mucosal invariant T cell" }, "cellTypeAuthorAnnotation": "MAIT, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 327.915443, "sdRefIntergenicDistribution": 1.245458, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 3017, "distinctRankCount": 39, "maxRank": 18067.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 171499603, "mappedReadsCount": 108600695, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138751" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0002063", "name": "type II pneumocyte" }, "cellTypeAuthorAnnotation": "AT2, Epithelia", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 1759.303552, "sdRefIntergenicDistribution": 1.025890, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 588, "distinctRankCount": 12, "maxRank": 17740.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 171499603, "mappedReadsCount": 108600695, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138751" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000987", "name": "IgA plasma cell" }, "cellTypeAuthorAnnotation": "B_plasma_IgA, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 640.763880, "sdRefIntergenicDistribution": 1.471082, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 2639, "distinctRankCount": 25, "maxRank": 17770.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 171499603, "mappedReadsCount": 108600695, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138751" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0019018", "name": "blood vessel smooth muscle cell" }, "cellTypeAuthorAnnotation": "Muscle_perivascular_immune_recruiting, Stroma", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 2128.204647, "sdRefIntergenicDistribution": 1.428533, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 770, "distinctRankCount": 17, "maxRank": 17760.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 171499603, "mappedReadsCount": 108600695, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138751" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0019018", "name": "blood vessel smooth muscle cell" }, "cellTypeAuthorAnnotation": "Muscle_smooth_arterial_systemic, Stroma", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 1543.209877, "sdRefIntergenicDistribution": 1.000000, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 0, "distinctRankCount": 0 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 171499603, "mappedReadsCount": 108600695, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138751" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000158", "name": "club cell" }, "cellTypeAuthorAnnotation": "Secretory_Club, Epithelia", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 58.055817, "sdRefIntergenicDistribution": 1.392034, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 18511, "distinctRankCount": 163, "maxRank": 19302.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 171499603, "mappedReadsCount": 108600695, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138751" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000787", "name": "memory B cell" }, "cellTypeAuthorAnnotation": "B_memory, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 278.859454, "sdRefIntergenicDistribution": 1.258009, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 3527, "distinctRankCount": 47, "maxRank": 18148.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 171499603, "mappedReadsCount": 108600695, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138751" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000784", "name": "plasmacytoid dendritic cell" }, "cellTypeAuthorAnnotation": "DC_plasmacytoid, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 245.058555, "sdRefIntergenicDistribution": 1.350503, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 4112, "distinctRankCount": 62, "maxRank": 18225.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 171499603, "mappedReadsCount": 108600695, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138751" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000067", "name": "ciliated epithelial cell" }, "cellTypeAuthorAnnotation": "Ciliated, Epithelia", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 63.642365, "sdRefIntergenicDistribution": 1.452675, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 16583, "distinctRankCount": 159, "maxRank": 19856.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 171499603, "mappedReadsCount": 108600695, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138751" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0009115", "name": "lymph node lymphatic vessel endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_Lymphatic, Vascular", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 5.659107, "sdRefIntergenicDistribution": 1.859198, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 265887, "distinctRankCount": 764, "maxRank": 23538.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 173613329, "mappedReadsCount": 115679411, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138755" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0002144", "name": "capillary endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_Cap_a, Vascular", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 3.599061, "sdRefIntergenicDistribution": 1.966346, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 470954, "distinctRankCount": 846, "maxRank": 24075.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 173613329, "mappedReadsCount": 115679411, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138755" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0002144", "name": "capillary endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_Cap_g, Vascular", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 1.937300, "sdRefIntergenicDistribution": 2.337814, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1301519, "distinctRankCount": 1602, "maxRank": 25154.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 173613329, "mappedReadsCount": 115679411, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138755" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000583", "name": "alveolar macrophage" }, "cellTypeAuthorAnnotation": "Macro_alveolar, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 5.539958, "sdRefIntergenicDistribution": 1.782477, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 248847, "distinctRankCount": 696, "maxRank": 22675.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 173613329, "mappedReadsCount": 115679411, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138755" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0002062", "name": "type I pneumocyte" }, "cellTypeAuthorAnnotation": "AT1 , Epithelia", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 2.892661, "sdRefIntergenicDistribution": 2.078498, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 646181, "distinctRankCount": 1195, "maxRank": 24533.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 173613329, "mappedReadsCount": 115679411, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138755" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000814", "name": "mature NK T cell" }, "cellTypeAuthorAnnotation": "NKT, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 23.136624, "sdRefIntergenicDistribution": 1.437706, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 46836, "distinctRankCount": 251, "maxRank": 20816.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 173613329, "mappedReadsCount": 115679411, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138755" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:1001568", "name": "pulmonary artery endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_arterial_pulmonary, Vascular", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 2.574864, "sdRefIntergenicDistribution": 2.061080, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 713447, "distinctRankCount": 1154, "maxRank": 24430.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 173613329, "mappedReadsCount": 115679411, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138755" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0009089", "name": "lung pericyte" }, "cellTypeAuthorAnnotation": "Muscle_pericyte_pulmonary, Stroma", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 3.654512, "sdRefIntergenicDistribution": 2.158170, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 557913, "distinctRankCount": 987, "maxRank": 24357.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 173613329, "mappedReadsCount": 115679411, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138755" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000798", "name": "gamma-delta T cell" }, "cellTypeAuthorAnnotation": "gdT, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 22.138572, "sdRefIntergenicDistribution": 1.483041, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 49397, "distinctRankCount": 256, "maxRank": 21055.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 173613329, "mappedReadsCount": 115679411, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138755" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000990", "name": "conventional dendritic cell" }, "cellTypeAuthorAnnotation": "DC_1, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 58.504540, "sdRefIntergenicDistribution": 1.384924, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 18394, "distinctRankCount": 155, "maxRank": 18911.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 173613329, "mappedReadsCount": 115679411, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138755" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000990", "name": "conventional dendritic cell" }, "cellTypeAuthorAnnotation": "DC_2, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 72.673713, "sdRefIntergenicDistribution": 1.440879, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 15158, "distinctRankCount": 130, "maxRank": 19251.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 173613329, "mappedReadsCount": 115679411, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138755" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0002543", "name": "vein endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_venous_pulmonary, Vascular", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 3.488836, "sdRefIntergenicDistribution": 1.708384, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 393565, "distinctRankCount": 806, "maxRank": 23612.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 173613329, "mappedReadsCount": 115679411, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138755" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0002543", "name": "vein endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_venous_systemic, Vascular", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 5.228300, "sdRefIntergenicDistribution": 1.642980, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 250674, "distinctRankCount": 725, "maxRank": 23114.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 173613329, "mappedReadsCount": 115679411, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138755" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000624", "name": "CD4-positive, alpha-beta T cell" }, "cellTypeAuthorAnnotation": "CD4_EM/Effector, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 17.237027, "sdRefIntergenicDistribution": 1.553992, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 65643, "distinctRankCount": 284, "maxRank": 21421.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 173613329, "mappedReadsCount": 115679411, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138755" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000624", "name": "CD4-positive, alpha-beta T cell" }, "cellTypeAuthorAnnotation": "CD4_naive/CM, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 104.895217, "sdRefIntergenicDistribution": 1.413609, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 9563, "distinctRankCount": 91, "maxRank": 18761.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 173613329, "mappedReadsCount": 115679411, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138755" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000057", "name": "fibroblast" }, "cellTypeAuthorAnnotation": "NAF_endoneurial, Stroma", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 125.839380, "sdRefIntergenicDistribution": 1.313654, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 8051, "distinctRankCount": 81, "maxRank": 18731.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 173613329, "mappedReadsCount": 115679411, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138755" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000057", "name": "fibroblast" }, "cellTypeAuthorAnnotation": "NAF_perineurial, Stroma", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 249.273727, "sdRefIntergenicDistribution": 1.227364, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 4040, "distinctRankCount": 48, "maxRank": 18335.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 173613329, "mappedReadsCount": 115679411, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138755" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0002553", "name": "fibroblast of lung" }, "cellTypeAuthorAnnotation": "Fibro_adventitial, Stroma", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 2.533054, "sdRefIntergenicDistribution": 2.283547, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 900651, "distinctRankCount": 1364, "maxRank": 24984.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 173613329, "mappedReadsCount": 115679411, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138755" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0002553", "name": "fibroblast of lung" }, "cellTypeAuthorAnnotation": "Fibro_alveolar, Stroma", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 2.228934, "sdRefIntergenicDistribution": 2.386718, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1235109, "distinctRankCount": 1629, "maxRank": 25300.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 173613329, "mappedReadsCount": 115679411, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138755" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0002553", "name": "fibroblast of lung" }, "cellTypeAuthorAnnotation": "Fibro_immune_recruiting, Stroma", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 99.763603, "sdRefIntergenicDistribution": 1.351397, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 10126, "distinctRankCount": 94, "maxRank": 18936.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 173613329, "mappedReadsCount": 115679411, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138755" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0002553", "name": "fibroblast of lung" }, "cellTypeAuthorAnnotation": "Fibro_peribronchial, Stroma", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 3.460016, "sdRefIntergenicDistribution": 2.127919, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 554083, "distinctRankCount": 1157, "maxRank": 24538.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 173613329, "mappedReadsCount": 115679411, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138755" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000192", "name": "smooth muscle cell" }, "cellTypeAuthorAnnotation": "Muscle_smooth_pulmonary, Stroma", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 2.971302, "sdRefIntergenicDistribution": 1.881290, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 536143, "distinctRankCount": 886, "maxRank": 24162.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 173613329, "mappedReadsCount": 115679411, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138755" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000913", "name": "effector memory CD8-positive, alpha-beta T cell" }, "cellTypeAuthorAnnotation": "CD8_EM, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 87.294199, "sdRefIntergenicDistribution": 1.414214, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 11744, "distinctRankCount": 117, "maxRank": 19066.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 173613329, "mappedReadsCount": 115679411, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138755" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000913", "name": "effector memory CD8-positive, alpha-beta T cell" }, "cellTypeAuthorAnnotation": "CD8_EM/EMRA, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 26.759471, "sdRefIntergenicDistribution": 1.412585, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 40095, "distinctRankCount": 227, "maxRank": 20552.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 173613329, "mappedReadsCount": 115679411, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138755" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0002633", "name": "respiratory basal cell" }, "cellTypeAuthorAnnotation": "Basal, Epithelia", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 7.786580, "sdRefIntergenicDistribution": 1.691656, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 166104, "distinctRankCount": 597, "maxRank": 23061.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 173613329, "mappedReadsCount": 115679411, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138755" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0002633", "name": "respiratory basal cell" }, "cellTypeAuthorAnnotation": "SMG_Basal, Epithelia", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 34.878289, "sdRefIntergenicDistribution": 1.441657, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 31505, "distinctRankCount": 228, "maxRank": 20387.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 173613329, "mappedReadsCount": 115679411, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138755" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0001054", "name": "CD14-positive monocyte" }, "cellTypeAuthorAnnotation": "Monocyte_CD14, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 612.968972, "sdRefIntergenicDistribution": 1.226854, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1605, "distinctRankCount": 17, "maxRank": 17893.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 173613329, "mappedReadsCount": 115679411, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138755" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000909", "name": "CD8-positive, alpha-beta memory T cell" }, "cellTypeAuthorAnnotation": "CD8_TRM, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 554.279886, "sdRefIntergenicDistribution": 1.258361, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1757, "distinctRankCount": 24, "maxRank": 17988.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 173613329, "mappedReadsCount": 115679411, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138755" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000909", "name": "CD8-positive, alpha-beta memory T cell" }, "cellTypeAuthorAnnotation": "CD8_TRM/EM, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 66.191380, "sdRefIntergenicDistribution": 1.341645, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 15397, "distinctRankCount": 128, "maxRank": 19533.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 173613329, "mappedReadsCount": 115679411, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138755" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0002396", "name": "CD14-low, CD16-positive monocyte" }, "cellTypeAuthorAnnotation": "Monocyte_CD16, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 155.812991, "sdRefIntergenicDistribution": 1.249518, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 6648, "distinctRankCount": 70, "maxRank": 18455.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 173613329, "mappedReadsCount": 115679411, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138755" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000186", "name": "myofibroblast cell" }, "cellTypeAuthorAnnotation": "Fibro_myofibroblast, Stroma", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 11.161644, "sdRefIntergenicDistribution": 1.540358, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 104957, "distinctRankCount": 372, "maxRank": 22388.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 173613329, "mappedReadsCount": 115679411, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138755" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000235", "name": "macrophage" }, "cellTypeAuthorAnnotation": "Macro_AW_CX3CR1, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 547.602417, "sdRefIntergenicDistribution": 1.329479, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1807, "distinctRankCount": 27, "maxRank": 17949.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 173613329, "mappedReadsCount": 115679411, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138755" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000623", "name": "natural killer cell" }, "cellTypeAuthorAnnotation": "NK_CD11d, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 1037.635048, "sdRefIntergenicDistribution": 1.169997, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 917, "distinctRankCount": 16, "maxRank": 17842.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 173613329, "mappedReadsCount": 115679411, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138755" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000623", "name": "natural killer cell" }, "cellTypeAuthorAnnotation": "NK_CD16hi, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 45.057068, "sdRefIntergenicDistribution": 1.350888, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 23220, "distinctRankCount": 153, "maxRank": 19965.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 173613329, "mappedReadsCount": 115679411, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138755" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000623", "name": "natural killer cell" }, "cellTypeAuthorAnnotation": "NK_CD56bright, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 157.299845, "sdRefIntergenicDistribution": 1.324316, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 6372, "distinctRankCount": 65, "maxRank": 18692.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 173613329, "mappedReadsCount": 115679411, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138755" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:1001603", "name": "lung macrophage" }, "cellTypeAuthorAnnotation": "Macro_CHIT1, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 146.412884, "sdRefIntergenicDistribution": 1.000000, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 0, "distinctRankCount": 0 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 173613329, "mappedReadsCount": 115679411, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138755" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:1001603", "name": "lung macrophage" }, "cellTypeAuthorAnnotation": "Macro_dividing, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 1396.648045, "sdRefIntergenicDistribution": 0.000000, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 0, "distinctRankCount": 0 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 173613329, "mappedReadsCount": 115679411, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138755" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:1001603", "name": "lung macrophage" }, "cellTypeAuthorAnnotation": "Macro_intermediate, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 299.297616, "sdRefIntergenicDistribution": 1.516131, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 3543, "distinctRankCount": 37, "maxRank": 18147.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 173613329, "mappedReadsCount": 115679411, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138755" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:1001603", "name": "lung macrophage" }, "cellTypeAuthorAnnotation": "Macro_interstitial, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 155.902369, "sdRefIntergenicDistribution": 1.454499, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 7091, "distinctRankCount": 68, "maxRank": 18596.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 173613329, "mappedReadsCount": 115679411, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138755" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:1001603", "name": "lung macrophage" }, "cellTypeAuthorAnnotation": "Macro_intravascular, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 23.145561, "sdRefIntergenicDistribution": 1.483814, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 47098, "distinctRankCount": 234, "maxRank": 20945.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 173613329, "mappedReadsCount": 115679411, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138755" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000897", "name": "CD4-positive, alpha-beta memory T cell" }, "cellTypeAuthorAnnotation": "CD4_TRM, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 462.981167, "sdRefIntergenicDistribution": 1.278120, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 2169, "distinctRankCount": 26, "maxRank": 17975.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 173613329, "mappedReadsCount": 115679411, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138755" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000077", "name": "mesothelial cell" }, "cellTypeAuthorAnnotation": "Mesothelia, Stroma", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 285.346634, "sdRefIntergenicDistribution": 1.224388, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 3363, "distinctRankCount": 30, "maxRank": 18252.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 173613329, "mappedReadsCount": 115679411, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138755" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000097", "name": "mast cell" }, "cellTypeAuthorAnnotation": "Mast_cell , Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 224.034148, "sdRefIntergenicDistribution": 1.305882, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 4605, "distinctRankCount": 49, "maxRank": 18334.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 173613329, "mappedReadsCount": 115679411, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138755" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:1000413", "name": "endothelial cell of artery" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_arterial_systemic, Vascular", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 64.861817, "sdRefIntergenicDistribution": 1.278099, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 15708, "distinctRankCount": 110, "maxRank": 19631.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 173613329, "mappedReadsCount": 115679411, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138755" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000940", "name": "mucosal invariant T cell" }, "cellTypeAuthorAnnotation": "MAIT, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 519.022111, "sdRefIntergenicDistribution": 1.243879, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1818, "distinctRankCount": 32, "maxRank": 17973.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 173613329, "mappedReadsCount": 115679411, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138755" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0002063", "name": "type II pneumocyte" }, "cellTypeAuthorAnnotation": "AT2, Epithelia", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 4.550539, "sdRefIntergenicDistribution": 1.751400, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 300279, "distinctRankCount": 822, "maxRank": 23199.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 173613329, "mappedReadsCount": 115679411, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138755" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0002063", "name": "type II pneumocyte" }, "cellTypeAuthorAnnotation": "Dividing_AT2, Epithelia", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 1538.461538, "sdRefIntergenicDistribution": 1.000000, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 0, "distinctRankCount": 0 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 173613329, "mappedReadsCount": 115679411, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138755" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0019018", "name": "blood vessel smooth muscle cell" }, "cellTypeAuthorAnnotation": "Muscle_perivascular_immune_recruiting, Stroma", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 114.980936, "sdRefIntergenicDistribution": 1.318962, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 8905, "distinctRankCount": 86, "maxRank": 18767.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 173613329, "mappedReadsCount": 115679411, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138755" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0019018", "name": "blood vessel smooth muscle cell" }, "cellTypeAuthorAnnotation": "Muscle_smooth_arterial_systemic, Stroma", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 35.154672, "sdRefIntergenicDistribution": 1.331152, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 30378, "distinctRankCount": 188, "maxRank": 20004.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 173613329, "mappedReadsCount": 115679411, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138755" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000158", "name": "club cell" }, "cellTypeAuthorAnnotation": "Secretory_Club, Epithelia", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 16.853728, "sdRefIntergenicDistribution": 1.675737, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 70735, "distinctRankCount": 346, "maxRank": 21148.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 173613329, "mappedReadsCount": 115679411, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138755" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000787", "name": "memory B cell" }, "cellTypeAuthorAnnotation": "B_memory, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 69.541914, "sdRefIntergenicDistribution": 1.356281, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 15058, "distinctRankCount": 134, "maxRank": 19164.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 173613329, "mappedReadsCount": 115679411, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138755" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000784", "name": "plasmacytoid dendritic cell" }, "cellTypeAuthorAnnotation": "DC_plasmacytoid, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 1368.694648, "sdRefIntergenicDistribution": 1.400910, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 644, "distinctRankCount": 10, "maxRank": 17749.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 173613329, "mappedReadsCount": 115679411, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138755" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000067", "name": "ciliated epithelial cell" }, "cellTypeAuthorAnnotation": "Ciliated, Epithelia", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 5.734157, "sdRefIntergenicDistribution": 1.897285, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 262063, "distinctRankCount": 1068, "maxRank": 24035.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 173613329, "mappedReadsCount": 115679411, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138755" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0009115", "name": "lymph node lymphatic vessel endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_Lymphatic, Vascular", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 4.239036, "sdRefIntergenicDistribution": 1.800286, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 343227, "distinctRankCount": 798, "maxRank": 23767.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 173613329, "mappedReadsCount": 115679411, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138755" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000985", "name": "IgG plasma cell" }, "cellTypeAuthorAnnotation": "B_plasma_IgG, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 4.947871, "sdRefIntergenicDistribution": 1.701257, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 259561, "distinctRankCount": 412, "maxRank": 21631.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 173613329, "mappedReadsCount": 115679411, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138755" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000160", "name": "goblet cell" }, "cellTypeAuthorAnnotation": "Secretory_Goblet, Epithelia", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 16.779405, "sdRefIntergenicDistribution": 1.481409, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 69425, "distinctRankCount": 299, "maxRank": 21072.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 173613329, "mappedReadsCount": 115679411, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138755" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0019019", "name": "tracheobronchial smooth muscle cell" }, "cellTypeAuthorAnnotation": "Muscle_smooth_airway, Stroma", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 142.175186, "sdRefIntergenicDistribution": 1.250092, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 7206, "distinctRankCount": 58, "maxRank": 18630.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 173613329, "mappedReadsCount": 115679411, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138755" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000815", "name": "regulatory T cell" }, "cellTypeAuthorAnnotation": "T_reg, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 771.542401, "sdRefIntergenicDistribution": 1.194611, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1194, "distinctRankCount": 16, "maxRank": 17867.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 173613329, "mappedReadsCount": 115679411, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138755" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0002368", "name": "respiratory epithelial cell" }, "cellTypeAuthorAnnotation": "Suprabasal, Epithelia", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 35.012090, "sdRefIntergenicDistribution": 1.444377, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 32192, "distinctRankCount": 228, "maxRank": 20089.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 173613329, "mappedReadsCount": 115679411, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138755" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000669", "name": "pericyte cell" }, "cellTypeAuthorAnnotation": "Muscle_pericyte_systemic, Stroma", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 179.413482, "sdRefIntergenicDistribution": 1.205462, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 5589, "distinctRankCount": 50, "maxRank": 18535.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 173613329, "mappedReadsCount": 115679411, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138755" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:4033044", "name": "deuterosomal cell" }, "cellTypeAuthorAnnotation": "Deuterosomal, Epithelia", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 96.994203, "sdRefIntergenicDistribution": 1.304055, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 10995, "distinctRankCount": 104, "maxRank": 18909.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 173613329, "mappedReadsCount": 115679411, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138755" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0001065", "name": "innate lymphoid cell" }, "cellTypeAuthorAnnotation": "ILC, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 722.484287, "sdRefIntergenicDistribution": 1.140995, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1323, "distinctRankCount": 20, "maxRank": 17892.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 418403395, "mappedReadsCount": 238718473, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138761" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:0000319", "name": "mucus secreting cell" }, "cellTypeAuthorAnnotation": "SMG_Mucous, Epithelia", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 0.769831, "sdRefIntergenicDistribution": 3.008046, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 7037293, "distinctRankCount": 7837, "maxRank": 27974.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 418403395, "mappedReadsCount": 238718473, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138761" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:0000138", "name": "chondrocyte" }, "cellTypeAuthorAnnotation": "Chondrocyte, Stroma", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 2.497145, "sdRefIntergenicDistribution": 2.011758, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 646860, "distinctRankCount": 4114, "maxRank": 25599.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 418403395, "mappedReadsCount": 238718473, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138761" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:1001603", "name": "lung macrophage" }, "cellTypeAuthorAnnotation": "Macro_CHIT1, Immune", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 45.052868, "sdRefIntergenicDistribution": 1.331693, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 23053, "distinctRankCount": 1299, "maxRank": 20369.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 418403395, "mappedReadsCount": 238718473, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138761" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:1001603", "name": "lung macrophage" }, "cellTypeAuthorAnnotation": "Macro_intermediate, Immune", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 39.083425, "sdRefIntergenicDistribution": 1.419380, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 27205, "distinctRankCount": 1112, "maxRank": 20295.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 418403395, "mappedReadsCount": 238718473, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138761" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:1001603", "name": "lung macrophage" }, "cellTypeAuthorAnnotation": "Macro_intravascular, Immune", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 11.472772, "sdRefIntergenicDistribution": 1.558818, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 100675, "distinctRankCount": 2195, "maxRank": 22269.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 418403395, "mappedReadsCount": 238718473, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138761" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:0000160", "name": "goblet cell" }, "cellTypeAuthorAnnotation": "Secretory_Goblet, Epithelia", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 6.285193, "sdRefIntergenicDistribution": 1.628999, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 196405, "distinctRankCount": 3262, "maxRank": 23558.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 418403395, "mappedReadsCount": 238718473, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138761" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:0000623", "name": "natural killer cell" }, "cellTypeAuthorAnnotation": "NK_CD16hi, Immune", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 93.551601, "sdRefIntergenicDistribution": 1.350749, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 11091, "distinctRankCount": 634, "maxRank": 19448.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 418403395, "mappedReadsCount": 238718473, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138761" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:0000623", "name": "natural killer cell" }, "cellTypeAuthorAnnotation": "NK_CD56bright, Immune", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 660.073688, "sdRefIntergenicDistribution": 1.323936, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1560, "distinctRankCount": 84, "maxRank": 18006.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 418403395, "mappedReadsCount": 238718473, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138761" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:0000158", "name": "club cell" }, "cellTypeAuthorAnnotation": "Secretory_Club, Epithelia", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 23.847030, "sdRefIntergenicDistribution": 1.369691, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 44914, "distinctRankCount": 1944, "maxRank": 21245.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 418403395, "mappedReadsCount": 238718473, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138761" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:0000909", "name": "CD8-positive, alpha-beta memory T cell" }, "cellTypeAuthorAnnotation": "CD8_TRM, Immune", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 347.785443, "sdRefIntergenicDistribution": 1.231352, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 2902, "distinctRankCount": 207, "maxRank": 18262.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 418403395, "mappedReadsCount": 238718473, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138761" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:0000909", "name": "CD8-positive, alpha-beta memory T cell" }, "cellTypeAuthorAnnotation": "CD8_TRM/EM, Immune", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 24.217871, "sdRefIntergenicDistribution": 1.474029, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 44730, "distinctRankCount": 1463, "maxRank": 21074.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 418403395, "mappedReadsCount": 238718473, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138761" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:0002553", "name": "fibroblast of lung" }, "cellTypeAuthorAnnotation": "Fibro_adventitial, Stroma", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 1.959226, "sdRefIntergenicDistribution": 1.999245, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 869357, "distinctRankCount": 4530, "maxRank": 26017.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 418403395, "mappedReadsCount": 238718473, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138761" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:0002553", "name": "fibroblast of lung" }, "cellTypeAuthorAnnotation": "Fibro_alveolar, Stroma", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 4.024194, "sdRefIntergenicDistribution": 1.730999, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 334720, "distinctRankCount": 3567, "maxRank": 24545.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 418403395, "mappedReadsCount": 238718473, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138761" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:0002553", "name": "fibroblast of lung" }, "cellTypeAuthorAnnotation": "Fibro_peribronchial, Stroma", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 11.598883, "sdRefIntergenicDistribution": 1.500241, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 96585, "distinctRankCount": 2271, "maxRank": 22279.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 418403395, "mappedReadsCount": 238718473, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138761" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:0002553", "name": "fibroblast of lung" }, "cellTypeAuthorAnnotation": "Fibro_perichondrial, Stroma", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 9.734725, "sdRefIntergenicDistribution": 1.538991, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 119542, "distinctRankCount": 2508, "maxRank": 22763.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 418403395, "mappedReadsCount": 238718473, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138761" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:0000787", "name": "memory B cell" }, "cellTypeAuthorAnnotation": "B_memory, Immune", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 43.070777, "sdRefIntergenicDistribution": 1.392781, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 24198, "distinctRankCount": 1055, "maxRank": 20258.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 418403395, "mappedReadsCount": 238718473, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138761" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:0000985", "name": "IgG plasma cell" }, "cellTypeAuthorAnnotation": "B_plasma_IgG, Immune", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 29.555451, "sdRefIntergenicDistribution": 1.632308, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 38547, "distinctRankCount": 1454, "maxRank": 20785.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 418403395, "mappedReadsCount": 238718473, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138761" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:0002633", "name": "respiratory basal cell" }, "cellTypeAuthorAnnotation": "Basal, Epithelia", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 4.174663, "sdRefIntergenicDistribution": 1.764331, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 327229, "distinctRankCount": 3595, "maxRank": 24677.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 418403395, "mappedReadsCount": 238718473, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138761" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:0002633", "name": "respiratory basal cell" }, "cellTypeAuthorAnnotation": "Dividing_Basal, Epithelia", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 23.115189, "sdRefIntergenicDistribution": 1.396142, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 46467, "distinctRankCount": 1995, "maxRank": 21457.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 418403395, "mappedReadsCount": 238718473, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138761" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:0002633", "name": "respiratory basal cell" }, "cellTypeAuthorAnnotation": "SMG_Basal, Epithelia", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 79.569055, "sdRefIntergenicDistribution": 1.285287, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 12850, "distinctRankCount": 785, "maxRank": 19361.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 418403395, "mappedReadsCount": 238718473, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138761" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:0000990", "name": "conventional dendritic cell" }, "cellTypeAuthorAnnotation": "DC_1, Immune", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 120.846388, "sdRefIntergenicDistribution": 1.314216, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 8417, "distinctRankCount": 623, "maxRank": 18759.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 418403395, "mappedReadsCount": 238718473, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138761" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:0000990", "name": "conventional dendritic cell" }, "cellTypeAuthorAnnotation": "DC_2, Immune", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 111.467485, "sdRefIntergenicDistribution": 1.207637, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 8972, "distinctRankCount": 603, "maxRank": 19019.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 418403395, "mappedReadsCount": 238718473, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138761" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:0000097", "name": "mast cell" }, "cellTypeAuthorAnnotation": "Mast_cell , Immune", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 21.449752, "sdRefIntergenicDistribution": 1.461686, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 50695, "distinctRankCount": 1750, "maxRank": 21243.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 418403395, "mappedReadsCount": 238718473, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138761" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:0000815", "name": "regulatory T cell" }, "cellTypeAuthorAnnotation": "T_reg, Immune", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 29.021237, "sdRefIntergenicDistribution": 1.448467, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 37142, "distinctRankCount": 1311, "maxRank": 20711.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 418403395, "mappedReadsCount": 238718473, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138761" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:0000192", "name": "smooth muscle cell" }, "cellTypeAuthorAnnotation": "Muscle_smooth_pulmonary, Stroma", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 236.234656, "sdRefIntergenicDistribution": 1.237959, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 4250, "distinctRankCount": 262, "maxRank": 18351.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 418403395, "mappedReadsCount": 238718473, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138761" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:0000897", "name": "CD4-positive, alpha-beta memory T cell" }, "cellTypeAuthorAnnotation": "CD4_TRM, Immune", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 559.639805, "sdRefIntergenicDistribution": 1.229409, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1777, "distinctRankCount": 44, "maxRank": 18083.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 418403395, "mappedReadsCount": 238718473, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138761" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:0000235", "name": "macrophage" }, "cellTypeAuthorAnnotation": "Macro_AW_CX3CR1, Immune", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 27.474715, "sdRefIntergenicDistribution": 1.358862, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 38280, "distinctRankCount": 1545, "maxRank": 20909.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 418403395, "mappedReadsCount": 238718473, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138761" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:0000067", "name": "ciliated epithelial cell" }, "cellTypeAuthorAnnotation": "Ciliated, Epithelia", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 5.930529, "sdRefIntergenicDistribution": 1.975944, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 239816, "distinctRankCount": 3665, "maxRank": 23895.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 418403395, "mappedReadsCount": 238718473, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138761" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:0001054", "name": "CD14-positive monocyte" }, "cellTypeAuthorAnnotation": "Monocyte_CD14, Immune", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 79.123294, "sdRefIntergenicDistribution": 1.252787, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 12914, "distinctRankCount": 802, "maxRank": 19551.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 418403395, "mappedReadsCount": 238718473, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138761" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:0000987", "name": "IgA plasma cell" }, "cellTypeAuthorAnnotation": "B_plasma_IgA, Immune", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 4.134907, "sdRefIntergenicDistribution": 1.870448, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 330023, "distinctRankCount": 3329, "maxRank": 24277.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 418403395, "mappedReadsCount": 238718473, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138761" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:0000146", "name": "simple columnar epithelial cell" }, "cellTypeAuthorAnnotation": "SMG_Duct, Epithelia", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 7.915716, "sdRefIntergenicDistribution": 1.576101, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 151459, "distinctRankCount": 2922, "maxRank": 23135.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 418403395, "mappedReadsCount": 238718473, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138761" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:4033044", "name": "deuterosomal cell" }, "cellTypeAuthorAnnotation": "Deuterosomal, Epithelia", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 21.910312, "sdRefIntergenicDistribution": 1.474286, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 50592, "distinctRankCount": 2004, "maxRank": 21013.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 418403395, "mappedReadsCount": 238718473, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138761" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:0000624", "name": "CD4-positive, alpha-beta T cell" }, "cellTypeAuthorAnnotation": "CD4_EM/Effector, Immune", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 17.428092, "sdRefIntergenicDistribution": 1.465167, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 62164, "distinctRankCount": 1632, "maxRank": 21524.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 418403395, "mappedReadsCount": 238718473, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138761" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:0000624", "name": "CD4-positive, alpha-beta T cell" }, "cellTypeAuthorAnnotation": "CD4_naive/CM, Immune", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 26.207147, "sdRefIntergenicDistribution": 1.411777, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 40550, "distinctRankCount": 1499, "maxRank": 20974.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 418403395, "mappedReadsCount": 238718473, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138761" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:0000583", "name": "alveolar macrophage" }, "cellTypeAuthorAnnotation": "Macro_alveolar, Immune", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 59.738914, "sdRefIntergenicDistribution": 1.347919, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 17266, "distinctRankCount": 823, "maxRank": 20010.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 418403395, "mappedReadsCount": 238718473, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138761" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:0000583", "name": "alveolar macrophage" }, "cellTypeAuthorAnnotation": "Macro_alveolar_metallothioneins, Immune", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 838.478974, "sdRefIntergenicDistribution": 1.027581, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1110, "distinctRankCount": 59, "maxRank": 17924.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 418403395, "mappedReadsCount": 238718473, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138761" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:0017000", "name": "pulmonary ionocyte" }, "cellTypeAuthorAnnotation": "Ionocyte_n_Brush, Epithelia", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 67.946026, "sdRefIntergenicDistribution": 1.337789, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 15165, "distinctRankCount": 1005, "maxRank": 19770.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 418403395, "mappedReadsCount": 238718473, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138761" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:0000798", "name": "gamma-delta T cell" }, "cellTypeAuthorAnnotation": "gdT, Immune", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 240.859661, "sdRefIntergenicDistribution": 1.323835, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 4152, "distinctRankCount": 238, "maxRank": 18457.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 418403395, "mappedReadsCount": 238718473, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138761" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:0002144", "name": "capillary endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_Cap_g, Vascular", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 216.533956, "sdRefIntergenicDistribution": 1.253539, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 4642, "distinctRankCount": 275, "maxRank": 18518.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 418403395, "mappedReadsCount": 238718473, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138761" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:0002368", "name": "respiratory epithelial cell" }, "cellTypeAuthorAnnotation": "Suprabasal, Epithelia", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 3.336391, "sdRefIntergenicDistribution": 1.836933, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 432830, "distinctRankCount": 4033, "maxRank": 24755.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 418403395, "mappedReadsCount": 238718473, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138761" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:0000940", "name": "mucosal invariant T cell" }, "cellTypeAuthorAnnotation": "MAIT, Immune", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 88.255689, "sdRefIntergenicDistribution": 1.336448, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 11473, "distinctRankCount": 619, "maxRank": 19429.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 418403395, "mappedReadsCount": 238718473, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138761" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:0000057", "name": "fibroblast" }, "cellTypeAuthorAnnotation": "NAF_endoneurial, Stroma", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 165.218530, "sdRefIntergenicDistribution": 1.201208, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 5997, "distinctRankCount": 379, "maxRank": 18581.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 418403395, "mappedReadsCount": 238718473, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138761" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:0000057", "name": "fibroblast" }, "cellTypeAuthorAnnotation": "NAF_perineurial, Stroma", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 68.399763, "sdRefIntergenicDistribution": 1.242682, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 14898, "distinctRankCount": 903, "maxRank": 19493.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 418403395, "mappedReadsCount": 238718473, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138761" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:0019018", "name": "blood vessel smooth muscle cell" }, "cellTypeAuthorAnnotation": "Muscle_perivascular_immune_recruiting, Stroma", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 36.034391, "sdRefIntergenicDistribution": 1.327803, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 28841, "distinctRankCount": 1274, "maxRank": 20424.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 418403395, "mappedReadsCount": 238718473, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138761" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:0019018", "name": "blood vessel smooth muscle cell" }, "cellTypeAuthorAnnotation": "Muscle_smooth_arterial_systemic, Stroma", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 38.952365, "sdRefIntergenicDistribution": 1.347580, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 26640, "distinctRankCount": 1156, "maxRank": 20099.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 418403395, "mappedReadsCount": 238718473, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138761" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:0002543", "name": "vein endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_venous_systemic, Vascular", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 70.646755, "sdRefIntergenicDistribution": 1.229385, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 14231, "distinctRankCount": 807, "maxRank": 19388.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 418403395, "mappedReadsCount": 238718473, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138761" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:0000788", "name": "naive B cell" }, "cellTypeAuthorAnnotation": "B_naive, Immune", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 163.202957, "sdRefIntergenicDistribution": 1.334970, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 6300, "distinctRankCount": 376, "maxRank": 18824.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 418403395, "mappedReadsCount": 238718473, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138761" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:1000413", "name": "endothelial cell of artery" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_arterial_systemic, Vascular", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 51.877785, "sdRefIntergenicDistribution": 1.459675, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 20740, "distinctRankCount": 1120, "maxRank": 19832.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 418403395, "mappedReadsCount": 238718473, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138761" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:0019001", "name": "tracheobronchial serous cell" }, "cellTypeAuthorAnnotation": "SMG_Serous, Epithelia", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 1.195900, "sdRefIntergenicDistribution": 2.370723, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 2054105, "distinctRankCount": 5781, "maxRank": 26811.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 418403395, "mappedReadsCount": 238718473, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138761" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:0009115", "name": "lymph node lymphatic vessel endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_Lymphatic, Vascular", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 94.174339, "sdRefIntergenicDistribution": 1.235100, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 10681, "distinctRankCount": 689, "maxRank": 19138.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 418403395, "mappedReadsCount": 238718473, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138761" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:0000980", "name": "plasmablast" }, "cellTypeAuthorAnnotation": "B_plasmablast, Immune", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 158.505690, "sdRefIntergenicDistribution": 1.458588, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 6777, "distinctRankCount": 423, "maxRank": 18752.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 418403395, "mappedReadsCount": 238718473, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138761" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:0019019", "name": "tracheobronchial smooth muscle cell" }, "cellTypeAuthorAnnotation": "Muscle_smooth_airway, Stroma", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 110.316678, "sdRefIntergenicDistribution": 1.302756, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 9500, "distinctRankCount": 592, "maxRank": 18754.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 418403395, "mappedReadsCount": 238718473, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138761" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:0000814", "name": "mature NK T cell" }, "cellTypeAuthorAnnotation": "NKT, Immune", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 1027.126148, "sdRefIntergenicDistribution": 1.305394, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1002, "distinctRankCount": 21, "maxRank": 17893.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 418403395, "mappedReadsCount": 238718473, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138761" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:0000165", "name": "neuroendocrine cell" }, "cellTypeAuthorAnnotation": "Neuroendocrine, Epithelia", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 107.245394, "sdRefIntergenicDistribution": 1.386655, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 9835, "distinctRankCount": 736, "maxRank": 19273.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 418403395, "mappedReadsCount": 238718473, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138761" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:0000669", "name": "pericyte cell" }, "cellTypeAuthorAnnotation": "Muscle_pericyte_systemic, Stroma", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 1885.520350, "sdRefIntergenicDistribution": 1.234643, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 532, "distinctRankCount": 23, "maxRank": 17730.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 418403395, "mappedReadsCount": 238718473, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138761" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:0000186", "name": "myofibroblast cell" }, "cellTypeAuthorAnnotation": "Fibro_myofibroblast, Stroma", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 303.929024, "sdRefIntergenicDistribution": 1.256569, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 3310, "distinctRankCount": 219, "maxRank": 18260.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 418403395, "mappedReadsCount": 238718473, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138761" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:0000077", "name": "mesothelial cell" }, "cellTypeAuthorAnnotation": "Mesothelia, Stroma", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 216.486732, "sdRefIntergenicDistribution": 1.199521, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 4576, "distinctRankCount": 308, "maxRank": 18433.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 418403395, "mappedReadsCount": 238718473, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138761" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:0002396", "name": "CD14-low, CD16-positive monocyte" }, "cellTypeAuthorAnnotation": "Monocyte_CD16, Immune", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 212.092645, "sdRefIntergenicDistribution": 1.234913, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 4720, "distinctRankCount": 257, "maxRank": 18615.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 418403395, "mappedReadsCount": 238718473, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138761" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:0000185", "name": "myoepithelial cell" }, "cellTypeAuthorAnnotation": "Myoepithelial, Epithelia", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 21.540340, "sdRefIntergenicDistribution": 1.380253, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 49110, "distinctRankCount": 1857, "maxRank": 21321.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 418403395, "mappedReadsCount": 238718473, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138761" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:0001065", "name": "innate lymphoid cell" }, "cellTypeAuthorAnnotation": "ILC, Immune", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 344.260696, "sdRefIntergenicDistribution": 1.260001, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 2963, "distinctRankCount": 157, "maxRank": 18233.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 418403395, "mappedReadsCount": 238718473, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138761" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:0000913", "name": "effector memory CD8-positive, alpha-beta T cell" }, "cellTypeAuthorAnnotation": "CD8_EM, Immune", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 11.262110, "sdRefIntergenicDistribution": 1.483147, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 99542, "distinctRankCount": 1937, "maxRank": 22271.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 418403395, "mappedReadsCount": 238718473, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138761" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:0000913", "name": "effector memory CD8-positive, alpha-beta T cell" }, "cellTypeAuthorAnnotation": "CD8_EM/EMRA, Immune", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 352.399194, "sdRefIntergenicDistribution": 1.392252, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 3005, "distinctRankCount": 140, "maxRank": 18286.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 418403395, "mappedReadsCount": 238718473, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138761" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:1001568", "name": "pulmonary artery endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_arterial_pulmonary, Vascular", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 131.796835, "sdRefIntergenicDistribution": 1.291581, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 7708, "distinctRankCount": 405, "maxRank": 18808.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 884068477, "mappedReadsCount": 527559253, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138767" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002144", "name": "capillary endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_Cap_a, Vascular", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 19.600075, "sdRefIntergenicDistribution": 1.421930, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 54944, "distinctRankCount": 1614, "maxRank": 21731.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 884068477, "mappedReadsCount": 527559253, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138767" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002144", "name": "capillary endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_Cap_g, Vascular", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 11.383897, "sdRefIntergenicDistribution": 1.510258, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 99576, "distinctRankCount": 2064, "maxRank": 22906.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 884068477, "mappedReadsCount": 527559253, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138767" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000067", "name": "ciliated epithelial cell" }, "cellTypeAuthorAnnotation": "Ciliated, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 9.718980, "sdRefIntergenicDistribution": 1.805210, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 130832, "distinctRankCount": 2818, "maxRank": 23463.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 884068477, "mappedReadsCount": 527559253, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138767" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002396", "name": "CD14-low, CD16-positive monocyte" }, "cellTypeAuthorAnnotation": "Monocyte_CD16, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 11.501099, "sdRefIntergenicDistribution": 1.490249, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 95654, "distinctRankCount": 1980, "maxRank": 22630.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 884068477, "mappedReadsCount": 527559253, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138767" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000909", "name": "CD8-positive, alpha-beta memory T cell" }, "cellTypeAuthorAnnotation": "CD8_TRM, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 6.377521, "sdRefIntergenicDistribution": 1.635199, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 190861, "distinctRankCount": 2754, "maxRank": 24291.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 884068477, "mappedReadsCount": 527559253, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138767" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000909", "name": "CD8-positive, alpha-beta memory T cell" }, "cellTypeAuthorAnnotation": "CD8_TRM/EM, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 14.247197, "sdRefIntergenicDistribution": 1.503906, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 77074, "distinctRankCount": 1830, "maxRank": 22330.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 884068477, "mappedReadsCount": 527559253, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138767" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000897", "name": "CD4-positive, alpha-beta memory T cell" }, "cellTypeAuthorAnnotation": "CD4_TRM, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 40.946695, "sdRefIntergenicDistribution": 1.275388, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 24075, "distinctRankCount": 897, "maxRank": 20527.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 884068477, "mappedReadsCount": 527559253, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138767" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000146", "name": "simple columnar epithelial cell" }, "cellTypeAuthorAnnotation": "SMG_Duct, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 9.880170, "sdRefIntergenicDistribution": 1.458484, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 113599, "distinctRankCount": 2200, "maxRank": 22581.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 884068477, "mappedReadsCount": 527559253, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138767" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000097", "name": "mast cell" }, "cellTypeAuthorAnnotation": "Mast_cell , Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 21.575193, "sdRefIntergenicDistribution": 1.437474, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 49408, "distinctRankCount": 1492, "maxRank": 21442.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 884068477, "mappedReadsCount": 527559253, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138767" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002633", "name": "respiratory basal cell" }, "cellTypeAuthorAnnotation": "Basal, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 9.853872, "sdRefIntergenicDistribution": 1.467342, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 113167, "distinctRankCount": 2273, "maxRank": 22868.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 884068477, "mappedReadsCount": 527559253, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138767" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000624", "name": "CD4-positive, alpha-beta T cell" }, "cellTypeAuthorAnnotation": "CD4_EM/Effector, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 3.856248, "sdRefIntergenicDistribution": 1.789666, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 352455, "distinctRankCount": 3036, "maxRank": 25394.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 884068477, "mappedReadsCount": 527559253, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138767" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000624", "name": "CD4-positive, alpha-beta T cell" }, "cellTypeAuthorAnnotation": "CD4_naive/CM, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 4.862626, "sdRefIntergenicDistribution": 1.739181, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 267768, "distinctRankCount": 2932, "maxRank": 24705.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 884068477, "mappedReadsCount": 527559253, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138767" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000583", "name": "alveolar macrophage" }, "cellTypeAuthorAnnotation": "Macro_alveolar, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 6.703315, "sdRefIntergenicDistribution": 1.653899, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 178148, "distinctRankCount": 2941, "maxRank": 23966.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 884068477, "mappedReadsCount": 527559253, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138767" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000815", "name": "regulatory T cell" }, "cellTypeAuthorAnnotation": "T_reg, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 25.127334, "sdRefIntergenicDistribution": 1.384030, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 41649, "distinctRankCount": 1371, "maxRank": 21447.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 884068477, "mappedReadsCount": 527559253, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138767" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002553", "name": "fibroblast of lung" }, "cellTypeAuthorAnnotation": "Fibro_adventitial, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 2.443337, "sdRefIntergenicDistribution": 1.865774, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 621731, "distinctRankCount": 4018, "maxRank": 25979.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 884068477, "mappedReadsCount": 527559253, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138767" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002553", "name": "fibroblast of lung" }, "cellTypeAuthorAnnotation": "Fibro_alveolar, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 2.094161, "sdRefIntergenicDistribution": 2.146605, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 899604, "distinctRankCount": 4464, "maxRank": 26512.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 884068477, "mappedReadsCount": 527559253, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138767" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002553", "name": "fibroblast of lung" }, "cellTypeAuthorAnnotation": "Fibro_peribronchial, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 11.248753, "sdRefIntergenicDistribution": 1.415464, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 97230, "distinctRankCount": 2154, "maxRank": 22648.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 884068477, "mappedReadsCount": 527559253, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138767" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002553", "name": "fibroblast of lung" }, "cellTypeAuthorAnnotation": "Fibro_perichondrial, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 56.179603, "sdRefIntergenicDistribution": 1.277609, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 18197, "distinctRankCount": 802, "maxRank": 19794.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 884068477, "mappedReadsCount": 527559253, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138767" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:1001603", "name": "lung macrophage" }, "cellTypeAuthorAnnotation": "Macro_CCL, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 688.416969, "sdRefIntergenicDistribution": 1.332762, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1471, "distinctRankCount": 53, "maxRank": 17942.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 884068477, "mappedReadsCount": 527559253, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138767" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:1001603", "name": "lung macrophage" }, "cellTypeAuthorAnnotation": "Macro_CHIT1, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 12.630392, "sdRefIntergenicDistribution": 1.513762, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 88848, "distinctRankCount": 2361, "maxRank": 22517.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 884068477, "mappedReadsCount": 527559253, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138767" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:1001603", "name": "lung macrophage" }, "cellTypeAuthorAnnotation": "Macro_dividing, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 1037.133596, "sdRefIntergenicDistribution": 1.195543, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 944, "distinctRankCount": 31, "maxRank": 17895.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 884068477, "mappedReadsCount": 527559253, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138767" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:1001603", "name": "lung macrophage" }, "cellTypeAuthorAnnotation": "Macro_intermediate, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 52.103149, "sdRefIntergenicDistribution": 1.281249, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 19080, "distinctRankCount": 908, "maxRank": 20098.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 884068477, "mappedReadsCount": 527559253, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138767" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:1001603", "name": "lung macrophage" }, "cellTypeAuthorAnnotation": "Macro_interstitial, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 85.852557, "sdRefIntergenicDistribution": 1.235373, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 11543, "distinctRankCount": 551, "maxRank": 19454.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 884068477, "mappedReadsCount": 527559253, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138767" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:1001603", "name": "lung macrophage" }, "cellTypeAuthorAnnotation": "Macro_intravascular, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 13.498528, "sdRefIntergenicDistribution": 1.466156, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 80090, "distinctRankCount": 2029, "maxRank": 22320.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 884068477, "mappedReadsCount": 527559253, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138767" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000623", "name": "natural killer cell" }, "cellTypeAuthorAnnotation": "NK_CD11d, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 60.411630, "sdRefIntergenicDistribution": 1.302134, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 16436, "distinctRankCount": 815, "maxRank": 20027.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 884068477, "mappedReadsCount": 527559253, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138767" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000623", "name": "natural killer cell" }, "cellTypeAuthorAnnotation": "NK_CD16hi, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 10.044101, "sdRefIntergenicDistribution": 1.574768, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 113546, "distinctRankCount": 2034, "maxRank": 23219.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 884068477, "mappedReadsCount": 527559253, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138767" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000623", "name": "natural killer cell" }, "cellTypeAuthorAnnotation": "NK_CD56bright, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 55.385960, "sdRefIntergenicDistribution": 1.303294, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 17830, "distinctRankCount": 908, "maxRank": 20181.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 884068477, "mappedReadsCount": 527559253, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138767" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000985", "name": "IgG plasma cell" }, "cellTypeAuthorAnnotation": "B_plasma_IgG, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 15.396925, "sdRefIntergenicDistribution": 1.562656, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 73471, "distinctRankCount": 1969, "maxRank": 22107.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 884068477, "mappedReadsCount": 527559253, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138767" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0009115", "name": "lymph node lymphatic vessel endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_Lymphatic, Vascular", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 9.680046, "sdRefIntergenicDistribution": 1.557122, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 117110, "distinctRankCount": 2554, "maxRank": 23307.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 884068477, "mappedReadsCount": 527559253, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138767" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000913", "name": "effector memory CD8-positive, alpha-beta T cell" }, "cellTypeAuthorAnnotation": "CD8_EM, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 14.734716, "sdRefIntergenicDistribution": 1.393589, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 71915, "distinctRankCount": 1686, "maxRank": 22396.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 884068477, "mappedReadsCount": 527559253, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138767" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000913", "name": "effector memory CD8-positive, alpha-beta T cell" }, "cellTypeAuthorAnnotation": "CD8_EM/EMRA, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 27.304092, "sdRefIntergenicDistribution": 1.368340, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 37480, "distinctRankCount": 1288, "maxRank": 21221.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 884068477, "mappedReadsCount": 527559253, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138767" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000186", "name": "myofibroblast cell" }, "cellTypeAuthorAnnotation": "Fibro_myofibroblast, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 54.697981, "sdRefIntergenicDistribution": 1.299845, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 18072, "distinctRankCount": 917, "maxRank": 20250.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 884068477, "mappedReadsCount": 527559253, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138767" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000158", "name": "club cell" }, "cellTypeAuthorAnnotation": "Secretory_Club, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 4.682418, "sdRefIntergenicDistribution": 1.676500, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 267420, "distinctRankCount": 3364, "maxRank": 24579.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 884068477, "mappedReadsCount": 527559253, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138767" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0001065", "name": "innate lymphoid cell" }, "cellTypeAuthorAnnotation": "ILC, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 97.370929, "sdRefIntergenicDistribution": 1.287948, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 10328, "distinctRankCount": 598, "maxRank": 19373.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 884068477, "mappedReadsCount": 527559253, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138767" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000192", "name": "smooth muscle cell" }, "cellTypeAuthorAnnotation": "Muscle_smooth_pulmonary, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 11.274529, "sdRefIntergenicDistribution": 1.465525, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 98533, "distinctRankCount": 2292, "maxRank": 22861.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 884068477, "mappedReadsCount": 527559253, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138767" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0019001", "name": "tracheobronchial serous cell" }, "cellTypeAuthorAnnotation": "SMG_Serous, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 1.474464, "sdRefIntergenicDistribution": 2.145037, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1328644, "distinctRankCount": 5078, "maxRank": 26444.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 884068477, "mappedReadsCount": 527559253, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138767" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0019019", "name": "tracheobronchial smooth muscle cell" }, "cellTypeAuthorAnnotation": "Muscle_smooth_airway, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 39.587178, "sdRefIntergenicDistribution": 1.317118, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 26190, "distinctRankCount": 1066, "maxRank": 20229.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 884068477, "mappedReadsCount": 527559253, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138767" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000990", "name": "conventional dendritic cell" }, "cellTypeAuthorAnnotation": "DC_1, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 47.426634, "sdRefIntergenicDistribution": 1.348099, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 21668, "distinctRankCount": 1152, "maxRank": 20101.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 884068477, "mappedReadsCount": 527559253, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138767" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000990", "name": "conventional dendritic cell" }, "cellTypeAuthorAnnotation": "DC_2, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 26.117651, "sdRefIntergenicDistribution": 1.421987, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 39310, "distinctRankCount": 1611, "maxRank": 21185.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 884068477, "mappedReadsCount": 527559253, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138767" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000990", "name": "conventional dendritic cell" }, "cellTypeAuthorAnnotation": "DC_activated, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 63.249253, "sdRefIntergenicDistribution": 1.430336, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 16195, "distinctRankCount": 870, "maxRank": 19669.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 884068477, "mappedReadsCount": 527559253, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138767" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0019018", "name": "blood vessel smooth muscle cell" }, "cellTypeAuthorAnnotation": "Muscle_perivascular_immune_recruiting, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 78.570105, "sdRefIntergenicDistribution": 1.260896, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 12967, "distinctRankCount": 631, "maxRank": 19281.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 884068477, "mappedReadsCount": 527559253, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138767" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0019018", "name": "blood vessel smooth muscle cell" }, "cellTypeAuthorAnnotation": "Muscle_smooth_arterial_systemic, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 41.351462, "sdRefIntergenicDistribution": 1.257173, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 24576, "distinctRankCount": 841, "maxRank": 19890.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 884068477, "mappedReadsCount": 527559253, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138767" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0001054", "name": "CD14-positive monocyte" }, "cellTypeAuthorAnnotation": "Monocyte_CD14, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 23.303636, "sdRefIntergenicDistribution": 1.391294, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 43851, "distinctRankCount": 1499, "maxRank": 21534.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 884068477, "mappedReadsCount": 527559253, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138767" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002063", "name": "type II pneumocyte" }, "cellTypeAuthorAnnotation": "AT2, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 0.909969, "sdRefIntergenicDistribution": 2.953192, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 5334267, "distinctRankCount": 7127, "maxRank": 28087.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 884068477, "mappedReadsCount": 527559253, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138767" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002063", "name": "type II pneumocyte" }, "cellTypeAuthorAnnotation": "Dividing_AT2, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 51.265265, "sdRefIntergenicDistribution": 1.334822, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 19236, "distinctRankCount": 1093, "maxRank": 20195.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 884068477, "mappedReadsCount": 527559253, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138767" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002543", "name": "vein endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_venous_pulmonary, Vascular", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 39.776749, "sdRefIntergenicDistribution": 1.300426, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 25070, "distinctRankCount": 1157, "maxRank": 20613.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 884068477, "mappedReadsCount": 527559253, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138767" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002543", "name": "vein endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_venous_systemic, Vascular", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 28.092163, "sdRefIntergenicDistribution": 1.305567, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 36155, "distinctRankCount": 1385, "maxRank": 20995.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 884068477, "mappedReadsCount": 527559253, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138767" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0009089", "name": "lung pericyte" }, "cellTypeAuthorAnnotation": "Muscle_pericyte_pulmonary, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 33.542421, "sdRefIntergenicDistribution": 1.307166, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 29649, "distinctRankCount": 1179, "maxRank": 20832.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 884068477, "mappedReadsCount": 527559253, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138767" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000814", "name": "mature NK T cell" }, "cellTypeAuthorAnnotation": "NKT, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 48.523855, "sdRefIntergenicDistribution": 1.297551, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 20455, "distinctRankCount": 914, "maxRank": 20352.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 884068477, "mappedReadsCount": 527559253, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138767" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000160", "name": "goblet cell" }, "cellTypeAuthorAnnotation": "Secretory_Goblet, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 30.528983, "sdRefIntergenicDistribution": 1.319412, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 33993, "distinctRankCount": 1524, "maxRank": 20639.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 884068477, "mappedReadsCount": 527559253, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138767" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000940", "name": "mucosal invariant T cell" }, "cellTypeAuthorAnnotation": "MAIT, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 27.501557, "sdRefIntergenicDistribution": 1.399000, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 36416, "distinctRankCount": 1206, "maxRank": 21175.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 884068477, "mappedReadsCount": 527559253, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138767" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000319", "name": "mucus secreting cell" }, "cellTypeAuthorAnnotation": "SMG_Mucous, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 1.456085, "sdRefIntergenicDistribution": 2.109232, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1302215, "distinctRankCount": 4873, "maxRank": 26245.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 884068477, "mappedReadsCount": 527559253, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138767" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:1001568", "name": "pulmonary artery endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_arterial_pulmonary, Vascular", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 35.344249, "sdRefIntergenicDistribution": 1.373116, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 29512, "distinctRankCount": 1270, "maxRank": 20910.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 884068477, "mappedReadsCount": 527559253, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138767" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000185", "name": "myoepithelial cell" }, "cellTypeAuthorAnnotation": "Myoepithelial, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 13.281222, "sdRefIntergenicDistribution": 1.405863, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 82419, "distinctRankCount": 2110, "maxRank": 21941.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 884068477, "mappedReadsCount": 527559253, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138767" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000798", "name": "gamma-delta T cell" }, "cellTypeAuthorAnnotation": "gdT, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 44.441363, "sdRefIntergenicDistribution": 1.314366, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 22928, "distinctRankCount": 937, "maxRank": 20441.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 884068477, "mappedReadsCount": 527559253, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138767" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0017000", "name": "pulmonary ionocyte" }, "cellTypeAuthorAnnotation": "Ionocyte_n_Brush, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 208.036158, "sdRefIntergenicDistribution": 1.288846, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 4816, "distinctRankCount": 214, "maxRank": 18450.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 884068477, "mappedReadsCount": 527559253, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138767" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000788", "name": "naive B cell" }, "cellTypeAuthorAnnotation": "B_naive, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 38.312028, "sdRefIntergenicDistribution": 1.360967, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 26340, "distinctRankCount": 1024, "maxRank": 20726.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 884068477, "mappedReadsCount": 527559253, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138767" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000235", "name": "macrophage" }, "cellTypeAuthorAnnotation": "Macro_AW_CX3CR1, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 32.177957, "sdRefIntergenicDistribution": 1.318847, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 31944, "distinctRankCount": 1281, "maxRank": 20728.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 884068477, "mappedReadsCount": 527559253, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138767" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000987", "name": "IgA plasma cell" }, "cellTypeAuthorAnnotation": "B_plasma_IgA, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 20.741161, "sdRefIntergenicDistribution": 1.542814, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 53113, "distinctRankCount": 1663, "maxRank": 21465.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 884068477, "mappedReadsCount": 527559253, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138767" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000057", "name": "fibroblast" }, "cellTypeAuthorAnnotation": "NAF_endoneurial, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 562.433263, "sdRefIntergenicDistribution": 1.182389, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1689, "distinctRankCount": 51, "maxRank": 17986.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 884068477, "mappedReadsCount": 527559253, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138767" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000057", "name": "fibroblast" }, "cellTypeAuthorAnnotation": "NAF_perineurial, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 460.054072, "sdRefIntergenicDistribution": 1.335303, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 2298, "distinctRankCount": 65, "maxRank": 18005.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 884068477, "mappedReadsCount": 527559253, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138767" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002376", "name": "non-myelinating Schwann cell" }, "cellTypeAuthorAnnotation": "Schwann_nonmyelinating, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 222.763332, "sdRefIntergenicDistribution": 1.123445, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 4330, "distinctRankCount": 210, "maxRank": 18352.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 884068477, "mappedReadsCount": 527559253, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138767" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000787", "name": "memory B cell" }, "cellTypeAuthorAnnotation": "B_memory, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 14.206621, "sdRefIntergenicDistribution": 1.512441, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 77175, "distinctRankCount": 1954, "maxRank": 22433.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 884068477, "mappedReadsCount": 527559253, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138767" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000138", "name": "chondrocyte" }, "cellTypeAuthorAnnotation": "Chondrocyte, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 48.362238, "sdRefIntergenicDistribution": 1.355079, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 21308, "distinctRankCount": 925, "maxRank": 19945.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 884068477, "mappedReadsCount": 527559253, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138767" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002368", "name": "respiratory epithelial cell" }, "cellTypeAuthorAnnotation": "Suprabasal, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 26.565971, "sdRefIntergenicDistribution": 1.370654, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 39984, "distinctRankCount": 1553, "maxRank": 20839.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 884068477, "mappedReadsCount": 527559253, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138767" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000165", "name": "neuroendocrine cell" }, "cellTypeAuthorAnnotation": "Neuroendocrine, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 131.854331, "sdRefIntergenicDistribution": 1.291053, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 7663, "distinctRankCount": 502, "maxRank": 18951.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 884068477, "mappedReadsCount": 527559253, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138767" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000077", "name": "mesothelial cell" }, "cellTypeAuthorAnnotation": "Mesothelia, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 33.193005, "sdRefIntergenicDistribution": 1.277570, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 31052, "distinctRankCount": 1378, "maxRank": 20813.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 884068477, "mappedReadsCount": 527559253, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138767" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:1000413", "name": "endothelial cell of artery" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_arterial_systemic, Vascular", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 139.474651, "sdRefIntergenicDistribution": 1.297212, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 7470, "distinctRankCount": 366, "maxRank": 18848.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 884068477, "mappedReadsCount": 527559253, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138767" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000784", "name": "plasmacytoid dendritic cell" }, "cellTypeAuthorAnnotation": "DC_plasmacytoid, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 333.675880, "sdRefIntergenicDistribution": 1.276446, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 2984, "distinctRankCount": 178, "maxRank": 18299.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 884068477, "mappedReadsCount": 527559253, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138767" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002062", "name": "type I pneumocyte" }, "cellTypeAuthorAnnotation": "AT1 , Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 1.643626, "sdRefIntergenicDistribution": 2.345386, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1310157, "distinctRankCount": 5140, "maxRank": 26676.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 171039817, "mappedReadsCount": 112038649, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138777" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0002144", "name": "capillary endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_Cap_a, Vascular", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 9.654057, "sdRefIntergenicDistribution": 1.630244, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 127892, "distinctRankCount": 354, "maxRank": 22373.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 171039817, "mappedReadsCount": 112038649, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138777" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0002144", "name": "capillary endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_Cap_g, Vascular", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 5.447810, "sdRefIntergenicDistribution": 1.927666, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 290915, "distinctRankCount": 642, "maxRank": 23645.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 171039817, "mappedReadsCount": 112038649, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138777" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0001054", "name": "CD14-positive monocyte" }, "cellTypeAuthorAnnotation": "Monocyte_CD14, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 3.940009, "sdRefIntergenicDistribution": 1.821771, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 348507, "distinctRankCount": 615, "maxRank": 22881.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 171039817, "mappedReadsCount": 112038649, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138777" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0002396", "name": "CD14-low, CD16-positive monocyte" }, "cellTypeAuthorAnnotation": "Monocyte_CD16, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 3.892172, "sdRefIntergenicDistribution": 1.835504, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 369438, "distinctRankCount": 684, "maxRank": 23008.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 171039817, "mappedReadsCount": 112038649, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138777" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0002543", "name": "vein endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_venous_pulmonary, Vascular", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 42.018845, "sdRefIntergenicDistribution": 1.356971, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 24597, "distinctRankCount": 168, "maxRank": 20057.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 171039817, "mappedReadsCount": 112038649, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138777" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0002543", "name": "vein endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_venous_systemic, Vascular", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 31.859741, "sdRefIntergenicDistribution": 1.310831, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 33303, "distinctRankCount": 218, "maxRank": 20216.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 171039817, "mappedReadsCount": 112038649, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138777" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0002553", "name": "fibroblast of lung" }, "cellTypeAuthorAnnotation": "Fibro_adventitial, Stroma", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 1.744042, "sdRefIntergenicDistribution": 2.272513, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1363708, "distinctRankCount": 1639, "maxRank": 25284.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 171039817, "mappedReadsCount": 112038649, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138777" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0002553", "name": "fibroblast of lung" }, "cellTypeAuthorAnnotation": "Fibro_alveolar, Stroma", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 15.382507, "sdRefIntergenicDistribution": 1.462607, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 73433, "distinctRankCount": 333, "maxRank": 21439.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 171039817, "mappedReadsCount": 112038649, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138777" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0002553", "name": "fibroblast of lung" }, "cellTypeAuthorAnnotation": "Fibro_immune_recruiting, Stroma", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 427.038675, "sdRefIntergenicDistribution": 1.487076, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 2718, "distinctRankCount": 50, "maxRank": 18041.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 171039817, "mappedReadsCount": 112038649, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138777" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0002553", "name": "fibroblast of lung" }, "cellTypeAuthorAnnotation": "Fibro_peribronchial, Stroma", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 84.837833, "sdRefIntergenicDistribution": 1.300534, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 11906, "distinctRankCount": 112, "maxRank": 19390.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 171039817, "mappedReadsCount": 112038649, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138777" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000623", "name": "natural killer cell" }, "cellTypeAuthorAnnotation": "NK_CD11d, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 52.646282, "sdRefIntergenicDistribution": 1.380524, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 20062, "distinctRankCount": 155, "maxRank": 19621.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 171039817, "mappedReadsCount": 112038649, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138777" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000623", "name": "natural killer cell" }, "cellTypeAuthorAnnotation": "NK_CD16hi, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 4.866158, "sdRefIntergenicDistribution": 1.828511, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 298669, "distinctRankCount": 587, "maxRank": 23248.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 171039817, "mappedReadsCount": 112038649, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138777" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000623", "name": "natural killer cell" }, "cellTypeAuthorAnnotation": "NK_CD56bright, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 32.383901, "sdRefIntergenicDistribution": 1.408036, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 32608, "distinctRankCount": 215, "maxRank": 20315.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 171039817, "mappedReadsCount": 112038649, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138777" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000990", "name": "conventional dendritic cell" }, "cellTypeAuthorAnnotation": "DC_1, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 4.836084, "sdRefIntergenicDistribution": 1.712992, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 284022, "distinctRankCount": 693, "maxRank": 22717.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 171039817, "mappedReadsCount": 112038649, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138777" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000990", "name": "conventional dendritic cell" }, "cellTypeAuthorAnnotation": "DC_2, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 5.525322, "sdRefIntergenicDistribution": 1.696137, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 240303, "distinctRankCount": 691, "maxRank": 22807.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 171039817, "mappedReadsCount": 112038649, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138777" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000990", "name": "conventional dendritic cell" }, "cellTypeAuthorAnnotation": "DC_activated, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 38.065934, "sdRefIntergenicDistribution": 1.448112, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 29038, "distinctRankCount": 215, "maxRank": 19627.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 171039817, "mappedReadsCount": 112038649, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138777" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:1001603", "name": "lung macrophage" }, "cellTypeAuthorAnnotation": "Macro_CHIT1, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 2.166799, "sdRefIntergenicDistribution": 2.039263, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 821984, "distinctRankCount": 1334, "maxRank": 24012.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 171039817, "mappedReadsCount": 112038649, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138777" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:1001603", "name": "lung macrophage" }, "cellTypeAuthorAnnotation": "Macro_intermediate, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 119.553270, "sdRefIntergenicDistribution": 1.374495, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 9125, "distinctRankCount": 82, "maxRank": 18724.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 171039817, "mappedReadsCount": 112038649, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138777" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:1001603", "name": "lung macrophage" }, "cellTypeAuthorAnnotation": "Macro_interstitial, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 3.964561, "sdRefIntergenicDistribution": 1.712643, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 341200, "distinctRankCount": 931, "maxRank": 22760.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 171039817, "mappedReadsCount": 112038649, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138777" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:1001603", "name": "lung macrophage" }, "cellTypeAuthorAnnotation": "Macro_intravascular, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 2.002951, "sdRefIntergenicDistribution": 2.173285, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1004459, "distinctRankCount": 1466, "maxRank": 24568.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 171039817, "mappedReadsCount": 112038649, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138777" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000158", "name": "club cell" }, "cellTypeAuthorAnnotation": "Secretory_Club, Epithelia", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 18.480935, "sdRefIntergenicDistribution": 1.500669, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 61759, "distinctRankCount": 245, "maxRank": 20313.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 171039817, "mappedReadsCount": 112038649, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138777" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000097", "name": "mast cell" }, "cellTypeAuthorAnnotation": "Mast_cell , Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 12.638075, "sdRefIntergenicDistribution": 1.489220, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 90823, "distinctRankCount": 335, "maxRank": 21600.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 171039817, "mappedReadsCount": 112038649, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138777" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000814", "name": "mature NK T cell" }, "cellTypeAuthorAnnotation": "NKT, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 4.086712, "sdRefIntergenicDistribution": 1.861226, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 371892, "distinctRankCount": 628, "maxRank": 23302.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 171039817, "mappedReadsCount": 112038649, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138777" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0002633", "name": "respiratory basal cell" }, "cellTypeAuthorAnnotation": "Basal, Epithelia", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 2.284425, "sdRefIntergenicDistribution": 2.011192, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 780184, "distinctRankCount": 1262, "maxRank": 25043.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 171039817, "mappedReadsCount": 112038649, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138777" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0002633", "name": "respiratory basal cell" }, "cellTypeAuthorAnnotation": "Dividing_Basal, Epithelia", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 15.343883, "sdRefIntergenicDistribution": 1.441070, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 74103, "distinctRankCount": 423, "maxRank": 21652.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 171039817, "mappedReadsCount": 112038649, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138777" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0002633", "name": "respiratory basal cell" }, "cellTypeAuthorAnnotation": "SMG_Basal, Epithelia", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 25.056242, "sdRefIntergenicDistribution": 1.425195, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 44199, "distinctRankCount": 286, "maxRank": 20918.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 171039817, "mappedReadsCount": 112038649, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138777" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000624", "name": "CD4-positive, alpha-beta T cell" }, "cellTypeAuthorAnnotation": "CD4_EM/Effector, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 4.006330, "sdRefIntergenicDistribution": 2.078410, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 464432, "distinctRankCount": 816, "maxRank": 23837.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 171039817, "mappedReadsCount": 112038649, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138777" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000624", "name": "CD4-positive, alpha-beta T cell" }, "cellTypeAuthorAnnotation": "CD4_naive/CM, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 14.157973, "sdRefIntergenicDistribution": 1.513226, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 80541, "distinctRankCount": 313, "maxRank": 21288.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 171039817, "mappedReadsCount": 112038649, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138777" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000897", "name": "CD4-positive, alpha-beta memory T cell" }, "cellTypeAuthorAnnotation": "CD4_TRM, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 4.422937, "sdRefIntergenicDistribution": 1.947455, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 363943, "distinctRankCount": 754, "maxRank": 23405.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 171039817, "mappedReadsCount": 112038649, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138777" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0019018", "name": "blood vessel smooth muscle cell" }, "cellTypeAuthorAnnotation": "Muscle_perivascular_immune_recruiting, Stroma", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 505.072975, "sdRefIntergenicDistribution": 1.299507, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 2176, "distinctRankCount": 38, "maxRank": 17873.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 171039817, "mappedReadsCount": 112038649, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138777" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0019018", "name": "blood vessel smooth muscle cell" }, "cellTypeAuthorAnnotation": "Muscle_smooth_arterial_systemic, Stroma", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 57.757639, "sdRefIntergenicDistribution": 1.231053, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 18064, "distinctRankCount": 122, "maxRank": 19409.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 171039817, "mappedReadsCount": 112038649, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138777" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000186", "name": "myofibroblast cell" }, "cellTypeAuthorAnnotation": "Fibro_myofibroblast, Stroma", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 22.178978, "sdRefIntergenicDistribution": 1.397412, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 48846, "distinctRankCount": 272, "maxRank": 20935.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 171039817, "mappedReadsCount": 112038649, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138777" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000909", "name": "CD8-positive, alpha-beta memory T cell" }, "cellTypeAuthorAnnotation": "CD8_TRM, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 33.675419, "sdRefIntergenicDistribution": 1.395876, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 31533, "distinctRankCount": 200, "maxRank": 20212.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 171039817, "mappedReadsCount": 112038649, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138777" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000909", "name": "CD8-positive, alpha-beta memory T cell" }, "cellTypeAuthorAnnotation": "CD8_TRM/EM, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 13.860918, "sdRefIntergenicDistribution": 1.577068, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 85382, "distinctRankCount": 346, "maxRank": 21579.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 171039817, "mappedReadsCount": 112038649, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138777" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000583", "name": "alveolar macrophage" }, "cellTypeAuthorAnnotation": "Macro_alveolar, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 1.472316, "sdRefIntergenicDistribution": 2.094893, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1265286, "distinctRankCount": 1500, "maxRank": 24336.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 171039817, "mappedReadsCount": 112038649, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138777" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000583", "name": "alveolar macrophage" }, "cellTypeAuthorAnnotation": "Macro_alveolar_metallothioneins, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 28.691048, "sdRefIntergenicDistribution": 1.600472, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 42207, "distinctRankCount": 214, "maxRank": 20011.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 171039817, "mappedReadsCount": 112038649, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138777" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000815", "name": "regulatory T cell" }, "cellTypeAuthorAnnotation": "T_reg, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 23.218006, "sdRefIntergenicDistribution": 1.453365, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 47719, "distinctRankCount": 266, "maxRank": 20865.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 171039817, "mappedReadsCount": 112038649, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138777" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000160", "name": "goblet cell" }, "cellTypeAuthorAnnotation": "Secretory_Goblet, Epithelia", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 5.756616, "sdRefIntergenicDistribution": 1.725231, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 232565, "distinctRankCount": 662, "maxRank": 22729.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 171039817, "mappedReadsCount": 112038649, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138777" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0001065", "name": "innate lymphoid cell" }, "cellTypeAuthorAnnotation": "ILC, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 15.561025, "sdRefIntergenicDistribution": 1.526567, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 74361, "distinctRankCount": 339, "maxRank": 21414.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 171039817, "mappedReadsCount": 112038649, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138777" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000192", "name": "smooth muscle cell" }, "cellTypeAuthorAnnotation": "Muscle_smooth_pulmonary, Stroma", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 24.179672, "sdRefIntergenicDistribution": 1.375403, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 44923, "distinctRankCount": 204, "maxRank": 20555.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 171039817, "mappedReadsCount": 112038649, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138777" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:1001568", "name": "pulmonary artery endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_arterial_pulmonary, Vascular", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 4.826047, "sdRefIntergenicDistribution": 1.821842, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 301948, "distinctRankCount": 751, "maxRank": 23540.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 171039817, "mappedReadsCount": 112038649, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138777" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000787", "name": "memory B cell" }, "cellTypeAuthorAnnotation": "B_memory, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 11.825121, "sdRefIntergenicDistribution": 1.553305, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 99295, "distinctRankCount": 382, "maxRank": 21540.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 171039817, "mappedReadsCount": 112038649, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138777" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000913", "name": "effector memory CD8-positive, alpha-beta T cell" }, "cellTypeAuthorAnnotation": "CD8_EM, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 16.894164, "sdRefIntergenicDistribution": 1.509152, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 67329, "distinctRankCount": 328, "maxRank": 21208.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 171039817, "mappedReadsCount": 112038649, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138777" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000913", "name": "effector memory CD8-positive, alpha-beta T cell" }, "cellTypeAuthorAnnotation": "CD8_EM/EMRA, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 3.383446, "sdRefIntergenicDistribution": 1.959350, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 490019, "distinctRankCount": 752, "maxRank": 23642.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 171039817, "mappedReadsCount": 112038649, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138777" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000985", "name": "IgG plasma cell" }, "cellTypeAuthorAnnotation": "B_plasma_IgG, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 4.174832, "sdRefIntergenicDistribution": 1.701861, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 301616, "distinctRankCount": 461, "maxRank": 21648.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 171039817, "mappedReadsCount": 112038649, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138777" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000784", "name": "plasmacytoid dendritic cell" }, "cellTypeAuthorAnnotation": "DC_plasmacytoid, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 40.019478, "sdRefIntergenicDistribution": 1.468773, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 26992, "distinctRankCount": 201, "maxRank": 19863.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 171039817, "mappedReadsCount": 112038649, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138777" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000987", "name": "IgA plasma cell" }, "cellTypeAuthorAnnotation": "B_plasma_IgA, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 4.609674, "sdRefIntergenicDistribution": 1.656692, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 269387, "distinctRankCount": 441, "maxRank": 21519.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 171039817, "mappedReadsCount": 112038649, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138777" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0009115", "name": "lymph node lymphatic vessel endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_Lymphatic, Vascular", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 16.243692, "sdRefIntergenicDistribution": 1.473706, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 69121, "distinctRankCount": 363, "maxRank": 21650.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 171039817, "mappedReadsCount": 112038649, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138777" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0002368", "name": "respiratory epithelial cell" }, "cellTypeAuthorAnnotation": "Suprabasal, Epithelia", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 5.807615, "sdRefIntergenicDistribution": 1.631673, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 219746, "distinctRankCount": 684, "maxRank": 23151.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 171039817, "mappedReadsCount": 112038649, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138777" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000067", "name": "ciliated epithelial cell" }, "cellTypeAuthorAnnotation": "Ciliated, Epithelia", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 7.489516, "sdRefIntergenicDistribution": 1.848276, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 187751, "distinctRankCount": 873, "maxRank": 23459.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 171039817, "mappedReadsCount": 112038649, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138777" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000940", "name": "mucosal invariant T cell" }, "cellTypeAuthorAnnotation": "MAIT, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 83.419276, "sdRefIntergenicDistribution": 1.305370, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 12253, "distinctRankCount": 113, "maxRank": 18867.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 171039817, "mappedReadsCount": 112038649, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138777" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0009089", "name": "lung pericyte" }, "cellTypeAuthorAnnotation": "Muscle_pericyte_pulmonary, Stroma", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 124.146742, "sdRefIntergenicDistribution": 1.228180, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 8116, "distinctRankCount": 65, "maxRank": 18859.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 171039817, "mappedReadsCount": 112038649, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138777" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:1000413", "name": "endothelial cell of artery" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_arterial_systemic, Vascular", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 49.697604, "sdRefIntergenicDistribution": 1.367432, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 20977, "distinctRankCount": 164, "maxRank": 19896.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 171039817, "mappedReadsCount": 112038649, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138777" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000235", "name": "macrophage" }, "cellTypeAuthorAnnotation": "Macro_AW_CX3CR1, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 45.543793, "sdRefIntergenicDistribution": 1.394985, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 24444, "distinctRankCount": 195, "maxRank": 19432.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 171039817, "mappedReadsCount": 112038649, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138777" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000669", "name": "pericyte cell" }, "cellTypeAuthorAnnotation": "Muscle_pericyte_systemic, Stroma", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 1880.338519, "sdRefIntergenicDistribution": 1.000000, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 0, "distinctRankCount": 0 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 171039817, "mappedReadsCount": 112038649, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138777" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000077", "name": "mesothelial cell" }, "cellTypeAuthorAnnotation": "Mesothelia, Stroma", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 160.396371, "sdRefIntergenicDistribution": 1.321352, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 6461, "distinctRankCount": 72, "maxRank": 18553.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 171039817, "mappedReadsCount": 112038649, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138777" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000165", "name": "neuroendocrine cell" }, "cellTypeAuthorAnnotation": "Neuroendocrine, Epithelia", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 238.993532, "sdRefIntergenicDistribution": 1.236407, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 4054, "distinctRankCount": 47, "maxRank": 18335.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 171039817, "mappedReadsCount": 112038649, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138777" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000057", "name": "fibroblast" }, "cellTypeAuthorAnnotation": "NAF_perineurial, Stroma", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 422.517648, "sdRefIntergenicDistribution": 1.169447, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 2192, "distinctRankCount": 23, "maxRank": 18069.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 171039817, "mappedReadsCount": 112038649, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138777" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000788", "name": "naive B cell" }, "cellTypeAuthorAnnotation": "B_naive, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 483.592503, "sdRefIntergenicDistribution": 1.239674, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 2073, "distinctRankCount": 41, "maxRank": 17931.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 171039817, "mappedReadsCount": 112038649, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138777" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000980", "name": "plasmablast" }, "cellTypeAuthorAnnotation": "B_plasmablast, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 121.540348, "sdRefIntergenicDistribution": 1.368676, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 9049, "distinctRankCount": 89, "maxRank": 18701.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 171039817, "mappedReadsCount": 112038649, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138777" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000798", "name": "gamma-delta T cell" }, "cellTypeAuthorAnnotation": "gdT, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 9.623493, "sdRefIntergenicDistribution": 1.645473, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 128800, "distinctRankCount": 427, "maxRank": 22131.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 378954393, "mappedReadsCount": 233848450, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138778" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0002144", "name": "capillary endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_Cap_a, Vascular", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 49.364951, "sdRefIntergenicDistribution": 1.513684, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 21581, "distinctRankCount": 1042, "maxRank": 20472.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 378954393, "mappedReadsCount": 233848450, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138778" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0002144", "name": "capillary endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_Cap_g, Vascular", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 45.955063, "sdRefIntergenicDistribution": 1.510479, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 23126, "distinctRankCount": 1091, "maxRank": 20602.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 378954393, "mappedReadsCount": 233848450, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138778" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000583", "name": "alveolar macrophage" }, "cellTypeAuthorAnnotation": "Macro_alveolar, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 34.292318, "sdRefIntergenicDistribution": 1.542182, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 32565, "distinctRankCount": 1449, "maxRank": 20921.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 378954393, "mappedReadsCount": 233848450, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138778" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0002062", "name": "type I pneumocyte" }, "cellTypeAuthorAnnotation": "AT1 , Epithelia", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 1.289611, "sdRefIntergenicDistribution": 2.469684, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1815286, "distinctRankCount": 6012, "maxRank": 26876.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 378954393, "mappedReadsCount": 233848450, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138778" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000814", "name": "mature NK T cell" }, "cellTypeAuthorAnnotation": "NKT, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 90.375538, "sdRefIntergenicDistribution": 1.359986, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 11593, "distinctRankCount": 605, "maxRank": 19539.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 378954393, "mappedReadsCount": 233848450, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138778" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:1001568", "name": "pulmonary artery endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_arterial_pulmonary, Vascular", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 43.613368, "sdRefIntergenicDistribution": 1.527405, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 24670, "distinctRankCount": 1110, "maxRank": 20690.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 378954393, "mappedReadsCount": 233848450, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138778" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0009089", "name": "lung pericyte" }, "cellTypeAuthorAnnotation": "Muscle_pericyte_pulmonary, Stroma", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 231.616020, "sdRefIntergenicDistribution": 1.246569, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 3822, "distinctRankCount": 479, "maxRank": 18589.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 378954393, "mappedReadsCount": 233848450, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138778" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000798", "name": "gamma-delta T cell" }, "cellTypeAuthorAnnotation": "gdT, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 550.400676, "sdRefIntergenicDistribution": 1.267329, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1885, "distinctRankCount": 127, "maxRank": 18092.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 378954393, "mappedReadsCount": 233848450, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138778" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000990", "name": "conventional dendritic cell" }, "cellTypeAuthorAnnotation": "DC_2, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 1835.229985, "sdRefIntergenicDistribution": 1.144345, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 512, "distinctRankCount": 15, "maxRank": 17768.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 378954393, "mappedReadsCount": 233848450, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138778" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0002543", "name": "vein endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_venous_pulmonary, Vascular", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 32.220259, "sdRefIntergenicDistribution": 1.528771, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 33547, "distinctRankCount": 1376, "maxRank": 21054.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 378954393, "mappedReadsCount": 233848450, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138778" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0002543", "name": "vein endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_venous_systemic, Vascular", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 146.109762, "sdRefIntergenicDistribution": 1.399250, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 6991, "distinctRankCount": 602, "maxRank": 19014.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 378954393, "mappedReadsCount": 233848450, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138778" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000624", "name": "CD4-positive, alpha-beta T cell" }, "cellTypeAuthorAnnotation": "CD4_EM/Effector, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 52.851669, "sdRefIntergenicDistribution": 1.400774, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 19825, "distinctRankCount": 978, "maxRank": 20557.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 378954393, "mappedReadsCount": 233848450, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138778" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000624", "name": "CD4-positive, alpha-beta T cell" }, "cellTypeAuthorAnnotation": "CD4_naive/CM, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 119.625057, "sdRefIntergenicDistribution": 1.391385, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 8774, "distinctRankCount": 473, "maxRank": 19283.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 378954393, "mappedReadsCount": 233848450, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138778" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0002553", "name": "fibroblast of lung" }, "cellTypeAuthorAnnotation": "Fibro_adventitial, Stroma", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 11.682557, "sdRefIntergenicDistribution": 1.602818, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 98046, "distinctRankCount": 2352, "maxRank": 23023.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 378954393, "mappedReadsCount": 233848450, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138778" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0002553", "name": "fibroblast of lung" }, "cellTypeAuthorAnnotation": "Fibro_alveolar, Stroma", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 4.172794, "sdRefIntergenicDistribution": 1.828594, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 315531, "distinctRankCount": 3271, "maxRank": 25014.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 378954393, "mappedReadsCount": 233848450, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138778" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0002553", "name": "fibroblast of lung" }, "cellTypeAuthorAnnotation": "Fibro_peribronchial, Stroma", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 142.845650, "sdRefIntergenicDistribution": 1.482804, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 7271, "distinctRankCount": 499, "maxRank": 19162.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 378954393, "mappedReadsCount": 233848450, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138778" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0002553", "name": "fibroblast of lung" }, "cellTypeAuthorAnnotation": "Fibro_perichondrial, Stroma", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 201.641050, "sdRefIntergenicDistribution": 1.419489, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 5199, "distinctRankCount": 411, "maxRank": 18780.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 378954393, "mappedReadsCount": 233848450, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138778" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000192", "name": "smooth muscle cell" }, "cellTypeAuthorAnnotation": "Muscle_smooth_pulmonary, Stroma", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 40.693224, "sdRefIntergenicDistribution": 1.552528, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 26448, "distinctRankCount": 1351, "maxRank": 20742.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 378954393, "mappedReadsCount": 233848450, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138778" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000913", "name": "effector memory CD8-positive, alpha-beta T cell" }, "cellTypeAuthorAnnotation": "CD8_EM, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 679.946163, "sdRefIntergenicDistribution": 1.246895, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1515, "distinctRankCount": 91, "maxRank": 17992.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 378954393, "mappedReadsCount": 233848450, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138778" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000913", "name": "effector memory CD8-positive, alpha-beta T cell" }, "cellTypeAuthorAnnotation": "CD8_EM/EMRA, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 397.779242, "sdRefIntergenicDistribution": 1.353455, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 2627, "distinctRankCount": 137, "maxRank": 18257.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 378954393, "mappedReadsCount": 233848450, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138778" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0002633", "name": "respiratory basal cell" }, "cellTypeAuthorAnnotation": "Basal, Epithelia", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 24.091074, "sdRefIntergenicDistribution": 1.445722, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 44748, "distinctRankCount": 1773, "maxRank": 21749.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 378954393, "mappedReadsCount": 233848450, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138778" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0002633", "name": "respiratory basal cell" }, "cellTypeAuthorAnnotation": "Dividing_Basal, Epithelia", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 157.244780, "sdRefIntergenicDistribution": 1.324735, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 6521, "distinctRankCount": 576, "maxRank": 18855.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 378954393, "mappedReadsCount": 233848450, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138778" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0001054", "name": "CD14-positive monocyte" }, "cellTypeAuthorAnnotation": "Monocyte_CD14, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 438.884677, "sdRefIntergenicDistribution": 1.556502, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 2543, "distinctRankCount": 138, "maxRank": 18302.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 378954393, "mappedReadsCount": 233848450, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138778" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000909", "name": "CD8-positive, alpha-beta memory T cell" }, "cellTypeAuthorAnnotation": "CD8_TRM, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 176.358322, "sdRefIntergenicDistribution": 1.295015, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 5790, "distinctRankCount": 419, "maxRank": 18794.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 378954393, "mappedReadsCount": 233848450, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138778" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000909", "name": "CD8-positive, alpha-beta memory T cell" }, "cellTypeAuthorAnnotation": "CD8_TRM/EM, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 190.612755, "sdRefIntergenicDistribution": 1.283867, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 5368, "distinctRankCount": 307, "maxRank": 18796.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 378954393, "mappedReadsCount": 233848450, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138778" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000186", "name": "myofibroblast cell" }, "cellTypeAuthorAnnotation": "Fibro_myofibroblast, Stroma", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 215.714062, "sdRefIntergenicDistribution": 1.347375, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 4765, "distinctRankCount": 340, "maxRank": 18701.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 378954393, "mappedReadsCount": 233848450, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138778" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000623", "name": "natural killer cell" }, "cellTypeAuthorAnnotation": "NK_CD11d, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 1610.705201, "sdRefIntergenicDistribution": 1.130040, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 576, "distinctRankCount": 33, "maxRank": 17786.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 378954393, "mappedReadsCount": 233848450, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138778" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000623", "name": "natural killer cell" }, "cellTypeAuthorAnnotation": "NK_CD16hi, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 68.320458, "sdRefIntergenicDistribution": 1.396639, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 15220, "distinctRankCount": 833, "maxRank": 20063.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 378954393, "mappedReadsCount": 233848450, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138778" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000623", "name": "natural killer cell" }, "cellTypeAuthorAnnotation": "NK_CD56bright, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 845.669427, "sdRefIntergenicDistribution": 1.454718, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1318, "distinctRankCount": 57, "maxRank": 17955.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 378954393, "mappedReadsCount": 233848450, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138778" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:1001603", "name": "lung macrophage" }, "cellTypeAuthorAnnotation": "Macro_CHIT1, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 131.655004, "sdRefIntergenicDistribution": 1.401450, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 8186, "distinctRankCount": 476, "maxRank": 19125.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 378954393, "mappedReadsCount": 233848450, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138778" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:1001603", "name": "lung macrophage" }, "cellTypeAuthorAnnotation": "Macro_intermediate, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 86.148439, "sdRefIntergenicDistribution": 1.343611, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 11995, "distinctRankCount": 621, "maxRank": 19594.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 378954393, "mappedReadsCount": 233848450, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138778" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:1001603", "name": "lung macrophage" }, "cellTypeAuthorAnnotation": "Macro_interstitial, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 537.070636, "sdRefIntergenicDistribution": 1.191558, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1857, "distinctRankCount": 85, "maxRank": 18057.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 378954393, "mappedReadsCount": 233848450, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138778" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:1001603", "name": "lung macrophage" }, "cellTypeAuthorAnnotation": "Macro_intravascular, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 164.407660, "sdRefIntergenicDistribution": 1.378049, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 6363, "distinctRankCount": 368, "maxRank": 18930.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 378954393, "mappedReadsCount": 233848450, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138778" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000897", "name": "CD4-positive, alpha-beta memory T cell" }, "cellTypeAuthorAnnotation": "CD4_TRM, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 1677.731919, "sdRefIntergenicDistribution": 1.030035, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 562, "distinctRankCount": 25, "maxRank": 17769.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 378954393, "mappedReadsCount": 233848450, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138778" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000077", "name": "mesothelial cell" }, "cellTypeAuthorAnnotation": "Mesothelia, Stroma", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 344.202370, "sdRefIntergenicDistribution": 1.659688, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 3258, "distinctRankCount": 216, "maxRank": 18356.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 378954393, "mappedReadsCount": 233848450, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138778" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000097", "name": "mast cell" }, "cellTypeAuthorAnnotation": "Mast_cell , Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 145.965930, "sdRefIntergenicDistribution": 1.377355, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 7064, "distinctRankCount": 437, "maxRank": 18937.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 378954393, "mappedReadsCount": 233848450, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138778" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000940", "name": "mucosal invariant T cell" }, "cellTypeAuthorAnnotation": "MAIT, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 2497.871330, "sdRefIntergenicDistribution": 1.311231, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 436, "distinctRankCount": 16, "maxRank": 17738.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 378954393, "mappedReadsCount": 233848450, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138778" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0002063", "name": "type II pneumocyte" }, "cellTypeAuthorAnnotation": "AT2, Epithelia", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 2.666453, "sdRefIntergenicDistribution": 2.001740, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 564564, "distinctRankCount": 4204, "maxRank": 25350.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 378954393, "mappedReadsCount": 233848450, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138778" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0002063", "name": "type II pneumocyte" }, "cellTypeAuthorAnnotation": "Dividing_AT2, Epithelia", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 372.893844, "sdRefIntergenicDistribution": 1.388052, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 2943, "distinctRankCount": 170, "maxRank": 18319.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 378954393, "mappedReadsCount": 233848450, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138778" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000987", "name": "IgA plasma cell" }, "cellTypeAuthorAnnotation": "B_plasma_IgA, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 251.920784, "sdRefIntergenicDistribution": 1.351096, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 4053, "distinctRankCount": 221, "maxRank": 18592.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 378954393, "mappedReadsCount": 233848450, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138778" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000158", "name": "club cell" }, "cellTypeAuthorAnnotation": "Secretory_Club, Epithelia", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 50.337404, "sdRefIntergenicDistribution": 1.413312, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 21104, "distinctRankCount": 1107, "maxRank": 20455.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 378954393, "mappedReadsCount": 233848450, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138778" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000787", "name": "memory B cell" }, "cellTypeAuthorAnnotation": "B_memory, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 935.681216, "sdRefIntergenicDistribution": 1.158406, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1042, "distinctRankCount": 63, "maxRank": 17916.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 378954393, "mappedReadsCount": 233848450, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138778" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000784", "name": "plasmacytoid dendritic cell" }, "cellTypeAuthorAnnotation": "DC_plasmacytoid, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 360.581363, "sdRefIntergenicDistribution": 1.222441, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 2798, "distinctRankCount": 134, "maxRank": 18289.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 378954393, "mappedReadsCount": 233848450, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138778" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000067", "name": "ciliated epithelial cell" }, "cellTypeAuthorAnnotation": "Ciliated, Epithelia", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 3.317738, "sdRefIntergenicDistribution": 2.167681, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 484652, "distinctRankCount": 4842, "maxRank": 25416.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 378954393, "mappedReadsCount": 233848450, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138778" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0009115", "name": "lymph node lymphatic vessel endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_Lymphatic, Vascular", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 5.759975, "sdRefIntergenicDistribution": 1.742897, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 217655, "distinctRankCount": 3267, "maxRank": 24509.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 378954393, "mappedReadsCount": 233848450, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138778" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000985", "name": "IgG plasma cell" }, "cellTypeAuthorAnnotation": "B_plasma_IgG, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 170.133199, "sdRefIntergenicDistribution": 1.388108, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 6257, "distinctRankCount": 363, "maxRank": 18819.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 378954393, "mappedReadsCount": 233848450, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138778" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0019019", "name": "tracheobronchial smooth muscle cell" }, "cellTypeAuthorAnnotation": "Muscle_smooth_airway, Stroma", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 275.936592, "sdRefIntergenicDistribution": 1.296986, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 3614, "distinctRankCount": 222, "maxRank": 18427.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 378954393, "mappedReadsCount": 233848450, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138778" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000815", "name": "regulatory T cell" }, "cellTypeAuthorAnnotation": "T_reg, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 877.528638, "sdRefIntergenicDistribution": 1.242598, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1155, "distinctRankCount": 37, "maxRank": 17969.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 378954393, "mappedReadsCount": 233848450, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138778" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0002368", "name": "respiratory epithelial cell" }, "cellTypeAuthorAnnotation": "Suprabasal, Epithelia", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 217.003291, "sdRefIntergenicDistribution": 1.250728, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 4451, "distinctRankCount": 361, "maxRank": 18644.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 378954393, "mappedReadsCount": 233848450, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138778" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000138", "name": "chondrocyte" }, "cellTypeAuthorAnnotation": "Chondrocyte, Stroma", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 28.811186, "sdRefIntergenicDistribution": 1.518600, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 36899, "distinctRankCount": 1798, "maxRank": 21396.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 378954393, "mappedReadsCount": 233848450, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138778" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000146", "name": "simple columnar epithelial cell" }, "cellTypeAuthorAnnotation": "SMG_Duct, Epithelia", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 68.348738, "sdRefIntergenicDistribution": 1.397750, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 15545, "distinctRankCount": 831, "maxRank": 19670.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 378954393, "mappedReadsCount": 233848450, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138778" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000165", "name": "neuroendocrine cell" }, "cellTypeAuthorAnnotation": "Neuroendocrine, Epithelia", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 83.828761, "sdRefIntergenicDistribution": 1.387844, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 12280, "distinctRankCount": 839, "maxRank": 19709.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 378954393, "mappedReadsCount": 233848450, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138778" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000319", "name": "mucus secreting cell" }, "cellTypeAuthorAnnotation": "SMG_Mucous, Epithelia", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 819.857121, "sdRefIntergenicDistribution": 1.277289, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1206, "distinctRankCount": 83, "maxRank": 17981.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 378954393, "mappedReadsCount": 233848450, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138778" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000788", "name": "naive B cell" }, "cellTypeAuthorAnnotation": "B_naive, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 755.233707, "sdRefIntergenicDistribution": 1.286523, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1338, "distinctRankCount": 44, "maxRank": 18011.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 185429388, "mappedReadsCount": 115723131, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138793" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0002144", "name": "capillary endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_Cap_a, Vascular", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 1872.659176, "sdRefIntergenicDistribution": 1.000000, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 0, "distinctRankCount": 0 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 185429388, "mappedReadsCount": 115723131, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138793" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0002144", "name": "capillary endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_Cap_g, Vascular", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 21.322656, "sdRefIntergenicDistribution": 1.513661, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 55182, "distinctRankCount": 345, "maxRank": 20849.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 185429388, "mappedReadsCount": 115723131, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138793" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000583", "name": "alveolar macrophage" }, "cellTypeAuthorAnnotation": "Macro_alveolar, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 2.223846, "sdRefIntergenicDistribution": 1.799969, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 660623, "distinctRankCount": 1181, "maxRank": 23643.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 185429388, "mappedReadsCount": 115723131, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138793" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000583", "name": "alveolar macrophage" }, "cellTypeAuthorAnnotation": "Macro_alveolar_metallothioneins, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 121.425995, "sdRefIntergenicDistribution": 1.231730, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 8592, "distinctRankCount": 82, "maxRank": 18582.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 185429388, "mappedReadsCount": 115723131, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138793" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000814", "name": "mature NK T cell" }, "cellTypeAuthorAnnotation": "NKT, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 3.417546, "sdRefIntergenicDistribution": 1.982722, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 490866, "distinctRankCount": 807, "maxRank": 23633.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 185429388, "mappedReadsCount": 115723131, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138793" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:1001568", "name": "pulmonary artery endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_arterial_pulmonary, Vascular", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 16.237896, "sdRefIntergenicDistribution": 1.658167, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 75258, "distinctRankCount": 514, "maxRank": 21516.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 185429388, "mappedReadsCount": 115723131, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138793" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000798", "name": "gamma-delta T cell" }, "cellTypeAuthorAnnotation": "gdT, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 4.858877, "sdRefIntergenicDistribution": 2.040189, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 337995, "distinctRankCount": 783, "maxRank": 23463.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 185429388, "mappedReadsCount": 115723131, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138793" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000990", "name": "conventional dendritic cell" }, "cellTypeAuthorAnnotation": "DC_1, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 186.546163, "sdRefIntergenicDistribution": 1.332286, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 5347, "distinctRankCount": 73, "maxRank": 18311.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 185429388, "mappedReadsCount": 115723131, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138793" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0002543", "name": "vein endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_venous_pulmonary, Vascular", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 38.908098, "sdRefIntergenicDistribution": 1.330338, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 28226, "distinctRankCount": 191, "maxRank": 19926.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 185429388, "mappedReadsCount": 115723131, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138793" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0002543", "name": "vein endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_venous_systemic, Vascular", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 49.365469, "sdRefIntergenicDistribution": 1.606768, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 24136, "distinctRankCount": 186, "maxRank": 19717.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 185429388, "mappedReadsCount": 115723131, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138793" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000624", "name": "CD4-positive, alpha-beta T cell" }, "cellTypeAuthorAnnotation": "CD4_EM/Effector, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 2.391715, "sdRefIntergenicDistribution": 2.828268, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1554831, "distinctRankCount": 1473, "maxRank": 25204.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 185429388, "mappedReadsCount": 115723131, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138793" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000624", "name": "CD4-positive, alpha-beta T cell" }, "cellTypeAuthorAnnotation": "CD4_naive/CM, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 2.867426, "sdRefIntergenicDistribution": 2.231088, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 705293, "distinctRankCount": 934, "maxRank": 24107.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 185429388, "mappedReadsCount": 115723131, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138793" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0002553", "name": "fibroblast of lung" }, "cellTypeAuthorAnnotation": "Fibro_adventitial, Stroma", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 1.494204, "sdRefIntergenicDistribution": 1.905390, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1080185, "distinctRankCount": 2064, "maxRank": 24727.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 185429388, "mappedReadsCount": 115723131, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138793" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0002553", "name": "fibroblast of lung" }, "cellTypeAuthorAnnotation": "Fibro_alveolar, Stroma", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 16.149159, "sdRefIntergenicDistribution": 1.372228, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 68558, "distinctRankCount": 357, "maxRank": 21374.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 185429388, "mappedReadsCount": 115723131, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138793" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000192", "name": "smooth muscle cell" }, "cellTypeAuthorAnnotation": "Muscle_smooth_pulmonary, Stroma", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 27.837756, "sdRefIntergenicDistribution": 1.408380, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 39288, "distinctRankCount": 247, "maxRank": 20490.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 185429388, "mappedReadsCount": 115723131, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138793" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000913", "name": "effector memory CD8-positive, alpha-beta T cell" }, "cellTypeAuthorAnnotation": "CD8_EM, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 4.483861, "sdRefIntergenicDistribution": 2.092009, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 384605, "distinctRankCount": 790, "maxRank": 23475.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 185429388, "mappedReadsCount": 115723131, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138793" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000913", "name": "effector memory CD8-positive, alpha-beta T cell" }, "cellTypeAuthorAnnotation": "CD8_EM/EMRA, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 2.237925, "sdRefIntergenicDistribution": 2.264418, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 966911, "distinctRankCount": 1193, "maxRank": 24346.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 185429388, "mappedReadsCount": 115723131, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138793" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0002633", "name": "respiratory basal cell" }, "cellTypeAuthorAnnotation": "Basal, Epithelia", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 1831.501832, "sdRefIntergenicDistribution": 1.000000, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 0, "distinctRankCount": 0 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 185429388, "mappedReadsCount": 115723131, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138793" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0001054", "name": "CD14-positive monocyte" }, "cellTypeAuthorAnnotation": "Monocyte_CD14, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 3.014757, "sdRefIntergenicDistribution": 2.195351, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 592732, "distinctRankCount": 865, "maxRank": 23414.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 185429388, "mappedReadsCount": 115723131, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138793" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000909", "name": "CD8-positive, alpha-beta memory T cell" }, "cellTypeAuthorAnnotation": "CD8_TRM, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 15.460873, "sdRefIntergenicDistribution": 1.711482, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 77384, "distinctRankCount": 349, "maxRank": 21580.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 185429388, "mappedReadsCount": 115723131, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138793" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000909", "name": "CD8-positive, alpha-beta memory T cell" }, "cellTypeAuthorAnnotation": "CD8_TRM/EM, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 3.533431, "sdRefIntergenicDistribution": 2.198204, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 543361, "distinctRankCount": 879, "maxRank": 23830.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 185429388, "mappedReadsCount": 115723131, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138793" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0002396", "name": "CD14-low, CD16-positive monocyte" }, "cellTypeAuthorAnnotation": "Monocyte_CD16, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 22.843692, "sdRefIntergenicDistribution": 1.627176, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 51677, "distinctRankCount": 279, "maxRank": 20271.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 185429388, "mappedReadsCount": 115723131, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138793" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000186", "name": "myofibroblast cell" }, "cellTypeAuthorAnnotation": "Fibro_myofibroblast, Stroma", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 29.791599, "sdRefIntergenicDistribution": 1.390563, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 36469, "distinctRankCount": 256, "maxRank": 20399.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 185429388, "mappedReadsCount": 115723131, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138793" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000235", "name": "macrophage" }, "cellTypeAuthorAnnotation": "Macro_AW_CX3CR1, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 561.640591, "sdRefIntergenicDistribution": 1.272751, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 2129, "distinctRankCount": 32, "maxRank": 17950.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 185429388, "mappedReadsCount": 115723131, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138793" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000623", "name": "natural killer cell" }, "cellTypeAuthorAnnotation": "NK_CD11d, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 63.443615, "sdRefIntergenicDistribution": 1.351187, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 16162, "distinctRankCount": 128, "maxRank": 19418.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 185429388, "mappedReadsCount": 115723131, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138793" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000623", "name": "natural killer cell" }, "cellTypeAuthorAnnotation": "NK_CD16hi, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 3.187551, "sdRefIntergenicDistribution": 2.196691, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 628553, "distinctRankCount": 1009, "maxRank": 24139.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 185429388, "mappedReadsCount": 115723131, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138793" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000623", "name": "natural killer cell" }, "cellTypeAuthorAnnotation": "NK_CD56bright, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 7.054028, "sdRefIntergenicDistribution": 1.832188, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 196433, "distinctRankCount": 576, "maxRank": 22719.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 185429388, "mappedReadsCount": 115723131, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138793" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:1001603", "name": "lung macrophage" }, "cellTypeAuthorAnnotation": "Macro_CCL, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 298.005375, "sdRefIntergenicDistribution": 1.338507, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 3098, "distinctRankCount": 40, "maxRank": 18069.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 185429388, "mappedReadsCount": 115723131, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138793" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:1001603", "name": "lung macrophage" }, "cellTypeAuthorAnnotation": "Macro_CHIT1, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 74.228162, "sdRefIntergenicDistribution": 1.446706, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 15490, "distinctRankCount": 107, "maxRank": 18886.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 185429388, "mappedReadsCount": 115723131, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138793" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:1001603", "name": "lung macrophage" }, "cellTypeAuthorAnnotation": "Macro_intermediate, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 8.746442, "sdRefIntergenicDistribution": 1.814646, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 153285, "distinctRankCount": 523, "maxRank": 21894.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 185429388, "mappedReadsCount": 115723131, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138793" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:1001603", "name": "lung macrophage" }, "cellTypeAuthorAnnotation": "Macro_interstitial, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 37.803987, "sdRefIntergenicDistribution": 1.458341, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 30485, "distinctRankCount": 207, "maxRank": 19548.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 185429388, "mappedReadsCount": 115723131, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138793" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:1001603", "name": "lung macrophage" }, "cellTypeAuthorAnnotation": "Macro_intravascular, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 21.931217, "sdRefIntergenicDistribution": 1.615629, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 54252, "distinctRankCount": 340, "maxRank": 20800.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 185429388, "mappedReadsCount": 115723131, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138793" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000897", "name": "CD4-positive, alpha-beta memory T cell" }, "cellTypeAuthorAnnotation": "CD4_TRM, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 3.847818, "sdRefIntergenicDistribution": 2.367078, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 559463, "distinctRankCount": 896, "maxRank": 23955.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 185429388, "mappedReadsCount": 115723131, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138793" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000077", "name": "mesothelial cell" }, "cellTypeAuthorAnnotation": "Mesothelia, Stroma", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 49.235198, "sdRefIntergenicDistribution": 1.289810, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 22335, "distinctRankCount": 182, "maxRank": 19748.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 185429388, "mappedReadsCount": 115723131, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138793" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000097", "name": "mast cell" }, "cellTypeAuthorAnnotation": "Mast_cell , Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 4.781887, "sdRefIntergenicDistribution": 2.090082, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 349597, "distinctRankCount": 680, "maxRank": 23297.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 185429388, "mappedReadsCount": 115723131, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138793" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000940", "name": "mucosal invariant T cell" }, "cellTypeAuthorAnnotation": "MAIT, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 16.402603, "sdRefIntergenicDistribution": 1.618067, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 71917, "distinctRankCount": 318, "maxRank": 21258.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 185429388, "mappedReadsCount": 115723131, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138793" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0002063", "name": "type II pneumocyte" }, "cellTypeAuthorAnnotation": "AT2, Epithelia", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 3.166967, "sdRefIntergenicDistribution": 1.680211, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 418991, "distinctRankCount": 843, "maxRank": 23393.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 185429388, "mappedReadsCount": 115723131, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138793" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0002063", "name": "type II pneumocyte" }, "cellTypeAuthorAnnotation": "Dividing_AT2, Epithelia", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 55.492962, "sdRefIntergenicDistribution": 1.403376, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 20198, "distinctRankCount": 183, "maxRank": 19474.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 185429388, "mappedReadsCount": 115723131, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138793" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000987", "name": "IgA plasma cell" }, "cellTypeAuthorAnnotation": "B_plasma_IgA, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 9.635779, "sdRefIntergenicDistribution": 1.650500, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 128710, "distinctRankCount": 368, "maxRank": 20964.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 185429388, "mappedReadsCount": 115723131, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138793" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0019018", "name": "blood vessel smooth muscle cell" }, "cellTypeAuthorAnnotation": "Muscle_smooth_arterial_systemic, Stroma", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 1109.877913, "sdRefIntergenicDistribution": 1.000000, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 0, "distinctRankCount": 0 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 185429388, "mappedReadsCount": 115723131, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138793" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000158", "name": "club cell" }, "cellTypeAuthorAnnotation": "Secretory_Club, Epithelia", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 79.193299, "sdRefIntergenicDistribution": 1.441235, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 14436, "distinctRankCount": 87, "maxRank": 18423.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 185429388, "mappedReadsCount": 115723131, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138793" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000787", "name": "memory B cell" }, "cellTypeAuthorAnnotation": "B_memory, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 3.397994, "sdRefIntergenicDistribution": 2.023510, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 498327, "distinctRankCount": 835, "maxRank": 23580.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 185429388, "mappedReadsCount": 115723131, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138793" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000784", "name": "plasmacytoid dendritic cell" }, "cellTypeAuthorAnnotation": "DC_plasmacytoid, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 1237.938226, "sdRefIntergenicDistribution": 1.232693, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 682, "distinctRankCount": 15, "maxRank": 17695.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 185429388, "mappedReadsCount": 115723131, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138793" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000067", "name": "ciliated epithelial cell" }, "cellTypeAuthorAnnotation": "Ciliated, Epithelia", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 175.617457, "sdRefIntergenicDistribution": 1.325967, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 6233, "distinctRankCount": 49, "maxRank": 18793.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 185429388, "mappedReadsCount": 115723131, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138793" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0009115", "name": "lymph node lymphatic vessel endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_Lymphatic, Vascular", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 38.497347, "sdRefIntergenicDistribution": 1.403211, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 28020, "distinctRankCount": 219, "maxRank": 20373.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 185429388, "mappedReadsCount": 115723131, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138793" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000985", "name": "IgG plasma cell" }, "cellTypeAuthorAnnotation": "B_plasma_IgG, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 7.156903, "sdRefIntergenicDistribution": 1.684285, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 180388, "distinctRankCount": 399, "maxRank": 21566.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 185429388, "mappedReadsCount": 115723131, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138793" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000815", "name": "regulatory T cell" }, "cellTypeAuthorAnnotation": "T_reg, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 15.550194, "sdRefIntergenicDistribution": 1.604390, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 75490, "distinctRankCount": 318, "maxRank": 21476.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 185429388, "mappedReadsCount": 115723131, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138793" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0001065", "name": "innate lymphoid cell" }, "cellTypeAuthorAnnotation": "ILC, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 17.733274, "sdRefIntergenicDistribution": 1.552447, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 63890, "distinctRankCount": 301, "maxRank": 21215.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 185429388, "mappedReadsCount": 115723131, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138793" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000788", "name": "naive B cell" }, "cellTypeAuthorAnnotation": "B_naive, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 25.326568, "sdRefIntergenicDistribution": 1.407847, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 42858, "distinctRankCount": 238, "maxRank": 20351.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 185429388, "mappedReadsCount": 115723131, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138793" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000980", "name": "plasmablast" }, "cellTypeAuthorAnnotation": "B_plasmablast, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 31.598770, "sdRefIntergenicDistribution": 1.427516, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 35836, "distinctRankCount": 294, "maxRank": 20105.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 185429388, "mappedReadsCount": 115723131, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138793" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000232", "name": "erythrocyte" }, "cellTypeAuthorAnnotation": "Erythrocyte, Vascular", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 818.853436, "sdRefIntergenicDistribution": 1.257538, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1127, "distinctRankCount": 22, "maxRank": 17812.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 962875983, "mappedReadsCount": 572954038, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138794" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002144", "name": "capillary endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_Cap_a, Vascular", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 49.924056, "sdRefIntergenicDistribution": 1.292478, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 20580, "distinctRankCount": 867, "maxRank": 20450.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 962875983, "mappedReadsCount": 572954038, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138794" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002144", "name": "capillary endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_Cap_g, Vascular", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 14.144602, "sdRefIntergenicDistribution": 1.431932, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 76384, "distinctRankCount": 1939, "maxRank": 22554.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 962875983, "mappedReadsCount": 572954038, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138794" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000067", "name": "ciliated epithelial cell" }, "cellTypeAuthorAnnotation": "Ciliated, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 2.086245, "sdRefIntergenicDistribution": 2.513172, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1046140, "distinctRankCount": 5382, "maxRank": 26725.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 962875983, "mappedReadsCount": 572954038, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138794" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002396", "name": "CD14-low, CD16-positive monocyte" }, "cellTypeAuthorAnnotation": "Monocyte_CD16, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 14.901759, "sdRefIntergenicDistribution": 1.438929, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 72590, "distinctRankCount": 1731, "maxRank": 22319.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 962875983, "mappedReadsCount": 572954038, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138794" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000909", "name": "CD8-positive, alpha-beta memory T cell" }, "cellTypeAuthorAnnotation": "CD8_TRM, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 5.983939, "sdRefIntergenicDistribution": 1.693001, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 206729, "distinctRankCount": 2660, "maxRank": 24151.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 962875983, "mappedReadsCount": 572954038, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138794" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000909", "name": "CD8-positive, alpha-beta memory T cell" }, "cellTypeAuthorAnnotation": "CD8_TRM/EM, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 13.644482, "sdRefIntergenicDistribution": 1.504614, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 81602, "distinctRankCount": 1770, "maxRank": 22406.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 962875983, "mappedReadsCount": 572954038, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138794" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000897", "name": "CD4-positive, alpha-beta memory T cell" }, "cellTypeAuthorAnnotation": "CD4_TRM, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 23.862836, "sdRefIntergenicDistribution": 1.456172, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 45196, "distinctRankCount": 1317, "maxRank": 21511.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 962875983, "mappedReadsCount": 572954038, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138794" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000146", "name": "simple columnar epithelial cell" }, "cellTypeAuthorAnnotation": "SMG_Duct, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 9.535409, "sdRefIntergenicDistribution": 1.561483, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 121108, "distinctRankCount": 2539, "maxRank": 23110.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 962875983, "mappedReadsCount": 572954038, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138794" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000097", "name": "mast cell" }, "cellTypeAuthorAnnotation": "Mast_cell , Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 9.377986, "sdRefIntergenicDistribution": 1.643455, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 125865, "distinctRankCount": 2297, "maxRank": 23579.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 962875983, "mappedReadsCount": 572954038, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138794" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002633", "name": "respiratory basal cell" }, "cellTypeAuthorAnnotation": "Basal, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 4.565992, "sdRefIntergenicDistribution": 1.795386, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 297719, "distinctRankCount": 3535, "maxRank": 25149.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 962875983, "mappedReadsCount": 572954038, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138794" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002633", "name": "respiratory basal cell" }, "cellTypeAuthorAnnotation": "Dividing_Basal, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 45.545790, "sdRefIntergenicDistribution": 1.300234, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 22446, "distinctRankCount": 1271, "maxRank": 20399.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 962875983, "mappedReadsCount": 572954038, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138794" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002633", "name": "respiratory basal cell" }, "cellTypeAuthorAnnotation": "SMG_Basal, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 664.373943, "sdRefIntergenicDistribution": 1.160858, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1486, "distinctRankCount": 64, "maxRank": 17943.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 962875983, "mappedReadsCount": 572954038, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138794" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000624", "name": "CD4-positive, alpha-beta T cell" }, "cellTypeAuthorAnnotation": "CD4_EM/Effector, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 4.739782, "sdRefIntergenicDistribution": 1.702789, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 269103, "distinctRankCount": 2663, "maxRank": 24956.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 962875983, "mappedReadsCount": 572954038, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138794" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000624", "name": "CD4-positive, alpha-beta T cell" }, "cellTypeAuthorAnnotation": "CD4_naive/CM, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 6.274071, "sdRefIntergenicDistribution": 1.636108, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 194174, "distinctRankCount": 2551, "maxRank": 24433.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 962875983, "mappedReadsCount": 572954038, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138794" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000583", "name": "alveolar macrophage" }, "cellTypeAuthorAnnotation": "Macro_alveolar, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 4.655386, "sdRefIntergenicDistribution": 1.710114, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 269139, "distinctRankCount": 3065, "maxRank": 24813.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 962875983, "mappedReadsCount": 572954038, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138794" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000583", "name": "alveolar macrophage" }, "cellTypeAuthorAnnotation": "Macro_alveolar_metallothioneins, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 389.416938, "sdRefIntergenicDistribution": 1.137179, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 2443, "distinctRankCount": 96, "maxRank": 18095.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 962875983, "mappedReadsCount": 572954038, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138794" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000815", "name": "regulatory T cell" }, "cellTypeAuthorAnnotation": "T_reg, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 27.213181, "sdRefIntergenicDistribution": 1.354522, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 38039, "distinctRankCount": 1230, "maxRank": 21291.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 962875983, "mappedReadsCount": 572954038, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138794" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002553", "name": "fibroblast of lung" }, "cellTypeAuthorAnnotation": "Fibro_adventitial, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 1.770869, "sdRefIntergenicDistribution": 2.119347, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1089323, "distinctRankCount": 4611, "maxRank": 26974.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 962875983, "mappedReadsCount": 572954038, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138794" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002553", "name": "fibroblast of lung" }, "cellTypeAuthorAnnotation": "Fibro_alveolar, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 2.109763, "sdRefIntergenicDistribution": 2.080370, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 838162, "distinctRankCount": 4415, "maxRank": 26647.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 962875983, "mappedReadsCount": 572954038, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138794" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002553", "name": "fibroblast of lung" }, "cellTypeAuthorAnnotation": "Fibro_peribronchial, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 6.867984, "sdRefIntergenicDistribution": 1.628934, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 178679, "distinctRankCount": 2982, "maxRank": 24054.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 962875983, "mappedReadsCount": 572954038, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138794" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002553", "name": "fibroblast of lung" }, "cellTypeAuthorAnnotation": "Fibro_perichondrial, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 10.024421, "sdRefIntergenicDistribution": 1.477175, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 111548, "distinctRankCount": 2371, "maxRank": 22955.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 962875983, "mappedReadsCount": 572954038, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138794" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:1001603", "name": "lung macrophage" }, "cellTypeAuthorAnnotation": "Macro_CCL, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 109.409970, "sdRefIntergenicDistribution": 1.363826, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 9550, "distinctRankCount": 555, "maxRank": 19034.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 962875983, "mappedReadsCount": 572954038, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138794" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:1001603", "name": "lung macrophage" }, "cellTypeAuthorAnnotation": "Macro_CHIT1, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 5.083868, "sdRefIntergenicDistribution": 1.629140, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 237197, "distinctRankCount": 3070, "maxRank": 24657.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 962875983, "mappedReadsCount": 572954038, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138794" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:1001603", "name": "lung macrophage" }, "cellTypeAuthorAnnotation": "Macro_intermediate, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 30.846095, "sdRefIntergenicDistribution": 1.364757, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 33637, "distinctRankCount": 1227, "maxRank": 21060.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 962875983, "mappedReadsCount": 572954038, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138794" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:1001603", "name": "lung macrophage" }, "cellTypeAuthorAnnotation": "Macro_interstitial, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 241.643174, "sdRefIntergenicDistribution": 1.232438, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 4097, "distinctRankCount": 168, "maxRank": 18470.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 962875983, "mappedReadsCount": 572954038, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138794" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:1001603", "name": "lung macrophage" }, "cellTypeAuthorAnnotation": "Macro_intravascular, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 10.745056, "sdRefIntergenicDistribution": 1.505526, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 104260, "distinctRankCount": 2057, "maxRank": 22929.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 962875983, "mappedReadsCount": 572954038, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138794" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000623", "name": "natural killer cell" }, "cellTypeAuthorAnnotation": "NK_CD11d, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 46.275804, "sdRefIntergenicDistribution": 1.391491, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 22564, "distinctRankCount": 962, "maxRank": 20659.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 962875983, "mappedReadsCount": 572954038, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138794" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000623", "name": "natural killer cell" }, "cellTypeAuthorAnnotation": "NK_CD16hi, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 10.879751, "sdRefIntergenicDistribution": 1.522132, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 102923, "distinctRankCount": 1925, "maxRank": 23353.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 962875983, "mappedReadsCount": 572954038, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138794" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000623", "name": "natural killer cell" }, "cellTypeAuthorAnnotation": "NK_CD56bright, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 92.216793, "sdRefIntergenicDistribution": 1.250977, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 10811, "distinctRankCount": 485, "maxRank": 19474.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 962875983, "mappedReadsCount": 572954038, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138794" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000985", "name": "IgG plasma cell" }, "cellTypeAuthorAnnotation": "B_plasma_IgG, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 8.510379, "sdRefIntergenicDistribution": 1.664788, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 141802, "distinctRankCount": 2568, "maxRank": 23407.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 962875983, "mappedReadsCount": 572954038, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138794" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0009115", "name": "lymph node lymphatic vessel endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_Lymphatic, Vascular", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 5.621548, "sdRefIntergenicDistribution": 1.680265, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 220956, "distinctRankCount": 3290, "maxRank": 24424.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 962875983, "mappedReadsCount": 572954038, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138794" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000913", "name": "effector memory CD8-positive, alpha-beta T cell" }, "cellTypeAuthorAnnotation": "CD8_EM, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 14.568674, "sdRefIntergenicDistribution": 1.435464, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 74235, "distinctRankCount": 1635, "maxRank": 22284.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 962875983, "mappedReadsCount": 572954038, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138794" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000913", "name": "effector memory CD8-positive, alpha-beta T cell" }, "cellTypeAuthorAnnotation": "CD8_EM/EMRA, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 41.844198, "sdRefIntergenicDistribution": 1.354884, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 24556, "distinctRankCount": 1004, "maxRank": 20642.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 962875983, "mappedReadsCount": 572954038, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138794" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000186", "name": "myofibroblast cell" }, "cellTypeAuthorAnnotation": "Fibro_myofibroblast, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 22.870216, "sdRefIntergenicDistribution": 1.425674, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 47316, "distinctRankCount": 1757, "maxRank": 21458.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 962875983, "mappedReadsCount": 572954038, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138794" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000158", "name": "club cell" }, "cellTypeAuthorAnnotation": "Secretory_Club, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 5.670061, "sdRefIntergenicDistribution": 1.620738, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 210159, "distinctRankCount": 2940, "maxRank": 24366.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 962875983, "mappedReadsCount": 572954038, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138794" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0001065", "name": "innate lymphoid cell" }, "cellTypeAuthorAnnotation": "ILC, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 165.600003, "sdRefIntergenicDistribution": 1.387110, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 6313, "distinctRankCount": 365, "maxRank": 18765.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 962875983, "mappedReadsCount": 572954038, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138794" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000192", "name": "smooth muscle cell" }, "cellTypeAuthorAnnotation": "Muscle_smooth_pulmonary, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 12.122742, "sdRefIntergenicDistribution": 1.439602, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 89446, "distinctRankCount": 2277, "maxRank": 22752.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 962875983, "mappedReadsCount": 572954038, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138794" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0019001", "name": "tracheobronchial serous cell" }, "cellTypeAuthorAnnotation": "SMG_Serous, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 1.649553, "sdRefIntergenicDistribution": 2.138508, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1150452, "distinctRankCount": 4911, "maxRank": 26523.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 962875983, "mappedReadsCount": 572954038, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138794" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0019019", "name": "tracheobronchial smooth muscle cell" }, "cellTypeAuthorAnnotation": "Muscle_smooth_airway, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 5.558426, "sdRefIntergenicDistribution": 1.640011, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 223200, "distinctRankCount": 2889, "maxRank": 24118.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 962875983, "mappedReadsCount": 572954038, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138794" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000990", "name": "conventional dendritic cell" }, "cellTypeAuthorAnnotation": "DC_1, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 39.670526, "sdRefIntergenicDistribution": 1.374263, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 26248, "distinctRankCount": 1101, "maxRank": 20290.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 962875983, "mappedReadsCount": 572954038, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138794" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000990", "name": "conventional dendritic cell" }, "cellTypeAuthorAnnotation": "DC_2, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 11.446978, "sdRefIntergenicDistribution": 1.479343, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 96775, "distinctRankCount": 2133, "maxRank": 22871.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 962875983, "mappedReadsCount": 572954038, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138794" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000990", "name": "conventional dendritic cell" }, "cellTypeAuthorAnnotation": "DC_activated, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 60.717736, "sdRefIntergenicDistribution": 1.370896, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 16679, "distinctRankCount": 699, "maxRank": 19683.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 962875983, "mappedReadsCount": 572954038, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138794" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0019018", "name": "blood vessel smooth muscle cell" }, "cellTypeAuthorAnnotation": "Muscle_perivascular_immune_recruiting, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 10.193325, "sdRefIntergenicDistribution": 1.479780, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 110124, "distinctRankCount": 2025, "maxRank": 22553.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 962875983, "mappedReadsCount": 572954038, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138794" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0019018", "name": "blood vessel smooth muscle cell" }, "cellTypeAuthorAnnotation": "Muscle_smooth_arterial_systemic, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 15.736342, "sdRefIntergenicDistribution": 1.402241, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 68503, "distinctRankCount": 1677, "maxRank": 21959.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 962875983, "mappedReadsCount": 572954038, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138794" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0001054", "name": "CD14-positive monocyte" }, "cellTypeAuthorAnnotation": "Monocyte_CD14, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 14.849633, "sdRefIntergenicDistribution": 1.374857, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 70101, "distinctRankCount": 1777, "maxRank": 22688.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 962875983, "mappedReadsCount": 572954038, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138794" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002063", "name": "type II pneumocyte" }, "cellTypeAuthorAnnotation": "AT2, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 0.900127, "sdRefIntergenicDistribution": 2.781390, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 4342947, "distinctRankCount": 6780, "maxRank": 28008.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 962875983, "mappedReadsCount": 572954038, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138794" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002063", "name": "type II pneumocyte" }, "cellTypeAuthorAnnotation": "Dividing_AT2, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 5.501323, "sdRefIntergenicDistribution": 1.622245, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 215528, "distinctRankCount": 3321, "maxRank": 24514.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 962875983, "mappedReadsCount": 572954038, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138794" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002543", "name": "vein endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_venous_pulmonary, Vascular", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 36.754517, "sdRefIntergenicDistribution": 1.355696, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 28015, "distinctRankCount": 1248, "maxRank": 20613.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 962875983, "mappedReadsCount": 572954038, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138794" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002543", "name": "vein endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_venous_systemic, Vascular", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 12.983775, "sdRefIntergenicDistribution": 1.429742, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 83827, "distinctRankCount": 1942, "maxRank": 22305.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 962875983, "mappedReadsCount": 572954038, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138794" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0009089", "name": "lung pericyte" }, "cellTypeAuthorAnnotation": "Muscle_pericyte_pulmonary, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 50.868283, "sdRefIntergenicDistribution": 1.339183, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 20328, "distinctRankCount": 994, "maxRank": 20232.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 962875983, "mappedReadsCount": 572954038, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138794" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000814", "name": "mature NK T cell" }, "cellTypeAuthorAnnotation": "NKT, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 44.137609, "sdRefIntergenicDistribution": 1.326909, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 23128, "distinctRankCount": 860, "maxRank": 20656.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 962875983, "mappedReadsCount": 572954038, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138794" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000160", "name": "goblet cell" }, "cellTypeAuthorAnnotation": "Secretory_Goblet, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 3.227614, "sdRefIntergenicDistribution": 1.913895, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 457892, "distinctRankCount": 4151, "maxRank": 25321.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 962875983, "mappedReadsCount": 572954038, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138794" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000940", "name": "mucosal invariant T cell" }, "cellTypeAuthorAnnotation": "MAIT, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 64.433201, "sdRefIntergenicDistribution": 1.277581, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 15569, "distinctRankCount": 652, "maxRank": 19969.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 962875983, "mappedReadsCount": 572954038, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138794" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000319", "name": "mucus secreting cell" }, "cellTypeAuthorAnnotation": "SMG_Mucous, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 1.746815, "sdRefIntergenicDistribution": 2.133754, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1064899, "distinctRankCount": 4828, "maxRank": 26535.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 962875983, "mappedReadsCount": 572954038, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138794" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:1001568", "name": "pulmonary artery endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_arterial_pulmonary, Vascular", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 16.926175, "sdRefIntergenicDistribution": 1.488691, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 64628, "distinctRankCount": 1855, "maxRank": 22165.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 962875983, "mappedReadsCount": 572954038, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138794" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000185", "name": "myoepithelial cell" }, "cellTypeAuthorAnnotation": "Myoepithelial, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 22.560842, "sdRefIntergenicDistribution": 1.350222, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 47103, "distinctRankCount": 1638, "maxRank": 21469.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 962875983, "mappedReadsCount": 572954038, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138794" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000798", "name": "gamma-delta T cell" }, "cellTypeAuthorAnnotation": "gdT, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 25.191967, "sdRefIntergenicDistribution": 1.471958, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 43095, "distinctRankCount": 1312, "maxRank": 21273.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 962875983, "mappedReadsCount": 572954038, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138794" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0017000", "name": "pulmonary ionocyte" }, "cellTypeAuthorAnnotation": "Ionocyte_n_Brush, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 70.445020, "sdRefIntergenicDistribution": 1.416103, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 15307, "distinctRankCount": 823, "maxRank": 19623.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 962875983, "mappedReadsCount": 572954038, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138794" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000788", "name": "naive B cell" }, "cellTypeAuthorAnnotation": "B_naive, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 67.383157, "sdRefIntergenicDistribution": 1.329391, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 15105, "distinctRankCount": 752, "maxRank": 19932.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 962875983, "mappedReadsCount": 572954038, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138794" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000235", "name": "macrophage" }, "cellTypeAuthorAnnotation": "Macro_AW_CX3CR1, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 23.009746, "sdRefIntergenicDistribution": 1.344068, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 44545, "distinctRankCount": 1647, "maxRank": 21554.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 962875983, "mappedReadsCount": 572954038, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138794" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000987", "name": "IgA plasma cell" }, "cellTypeAuthorAnnotation": "B_plasma_IgA, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 12.847964, "sdRefIntergenicDistribution": 1.608301, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 89241, "distinctRankCount": 1959, "maxRank": 22431.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 962875983, "mappedReadsCount": 572954038, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138794" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000057", "name": "fibroblast" }, "cellTypeAuthorAnnotation": "NAF_endoneurial, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 97.595963, "sdRefIntergenicDistribution": 1.281079, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 10662, "distinctRankCount": 540, "maxRank": 19201.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 962875983, "mappedReadsCount": 572954038, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138794" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000057", "name": "fibroblast" }, "cellTypeAuthorAnnotation": "NAF_perineurial, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 27.487966, "sdRefIntergenicDistribution": 1.375927, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 37870, "distinctRankCount": 1505, "maxRank": 21054.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 962875983, "mappedReadsCount": 572954038, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138794" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002376", "name": "non-myelinating Schwann cell" }, "cellTypeAuthorAnnotation": "Schwann_nonmyelinating, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 33.278230, "sdRefIntergenicDistribution": 1.353692, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 31206, "distinctRankCount": 1170, "maxRank": 20801.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 962875983, "mappedReadsCount": 572954038, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138794" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000787", "name": "memory B cell" }, "cellTypeAuthorAnnotation": "B_memory, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 29.290458, "sdRefIntergenicDistribution": 1.437985, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 36751, "distinctRankCount": 1266, "maxRank": 21049.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 962875983, "mappedReadsCount": 572954038, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138794" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000138", "name": "chondrocyte" }, "cellTypeAuthorAnnotation": "Chondrocyte, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 2.949671, "sdRefIntergenicDistribution": 1.882441, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 509875, "distinctRankCount": 4068, "maxRank": 25713.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 962875983, "mappedReadsCount": 572954038, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138794" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002368", "name": "respiratory epithelial cell" }, "cellTypeAuthorAnnotation": "Suprabasal, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 4.473866, "sdRefIntergenicDistribution": 1.768905, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 298459, "distinctRankCount": 3630, "maxRank": 24739.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 962875983, "mappedReadsCount": 572954038, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138794" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000165", "name": "neuroendocrine cell" }, "cellTypeAuthorAnnotation": "Neuroendocrine, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 109.891382, "sdRefIntergenicDistribution": 1.319833, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 8992, "distinctRankCount": 620, "maxRank": 19197.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 962875983, "mappedReadsCount": 572954038, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138794" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000077", "name": "mesothelial cell" }, "cellTypeAuthorAnnotation": "Mesothelia, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 65.456214, "sdRefIntergenicDistribution": 1.435049, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 16279, "distinctRankCount": 1042, "maxRank": 19703.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 962875983, "mappedReadsCount": 572954038, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138794" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:1000413", "name": "endothelial cell of artery" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_arterial_systemic, Vascular", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 70.271370, "sdRefIntergenicDistribution": 1.258776, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 14134, "distinctRankCount": 736, "maxRank": 19553.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 962875983, "mappedReadsCount": 572954038, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138794" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000784", "name": "plasmacytoid dendritic cell" }, "cellTypeAuthorAnnotation": "DC_plasmacytoid, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 308.553131, "sdRefIntergenicDistribution": 1.143116, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 3086, "distinctRankCount": 99, "maxRank": 18386.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 962875983, "mappedReadsCount": 572954038, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138794" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002062", "name": "type I pneumocyte" }, "cellTypeAuthorAnnotation": "AT1 , Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 1.849652, "sdRefIntergenicDistribution": 2.175316, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 983585, "distinctRankCount": 4609, "maxRank": 26515.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 962875983, "mappedReadsCount": 572954038, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138794" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0019002", "name": "tracheobronchial chondrocyte" }, "cellTypeAuthorAnnotation": "Chondrocyte, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 168.371008, "sdRefIntergenicDistribution": 1.335258, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 6212, "distinctRankCount": 299, "maxRank": 18558.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 962875983, "mappedReadsCount": 572954038, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138794" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:4033044", "name": "deuterosomal cell" }, "cellTypeAuthorAnnotation": "Deuterosomal, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 10.074291, "sdRefIntergenicDistribution": 1.728744, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 123885, "distinctRankCount": 2885, "maxRank": 22819.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 962875983, "mappedReadsCount": 572954038, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138794" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000218", "name": "myelinating Schwann cell" }, "cellTypeAuthorAnnotation": "Schwann_Myelinating, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 647.174323, "sdRefIntergenicDistribution": 1.348704, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1644, "distinctRankCount": 61, "maxRank": 17946.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 962875983, "mappedReadsCount": 572954038, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138794" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000669", "name": "pericyte cell" }, "cellTypeAuthorAnnotation": "Muscle_pericyte_systemic, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 221.430709, "sdRefIntergenicDistribution": 1.261866, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 4433, "distinctRankCount": 297, "maxRank": 18551.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 962875983, "mappedReadsCount": 572954038, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138794" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000980", "name": "plasmablast" }, "cellTypeAuthorAnnotation": "B_plasmablast, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 309.155894, "sdRefIntergenicDistribution": 1.200108, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 3136, "distinctRankCount": 199, "maxRank": 18321.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 190252011, "mappedReadsCount": 143490748, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138796" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0002144", "name": "capillary endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_Cap_a, Vascular", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 351.609133, "sdRefIntergenicDistribution": 1.260218, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 3044, "distinctRankCount": 32, "maxRank": 18197.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 190252011, "mappedReadsCount": 143490748, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138796" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0002144", "name": "capillary endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_Cap_g, Vascular", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 569.931046, "sdRefIntergenicDistribution": 1.128420, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1847, "distinctRankCount": 27, "maxRank": 18004.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 190252011, "mappedReadsCount": 143490748, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138796" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000583", "name": "alveolar macrophage" }, "cellTypeAuthorAnnotation": "Macro_alveolar, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 2.477578, "sdRefIntergenicDistribution": 1.833185, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 579214, "distinctRankCount": 928, "maxRank": 23375.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 190252011, "mappedReadsCount": 143490748, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138796" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000583", "name": "alveolar macrophage" }, "cellTypeAuthorAnnotation": "Macro_alveolar_metallothioneins, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 49.229748, "sdRefIntergenicDistribution": 1.593021, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 25306, "distinctRankCount": 158, "maxRank": 19335.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 190252011, "mappedReadsCount": 143490748, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138796" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0002062", "name": "type I pneumocyte" }, "cellTypeAuthorAnnotation": "AT1 , Epithelia", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 146.001554, "sdRefIntergenicDistribution": 1.243854, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 7332, "distinctRankCount": 66, "maxRank": 18178.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 190252011, "mappedReadsCount": 143490748, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138796" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000814", "name": "mature NK T cell" }, "cellTypeAuthorAnnotation": "NKT, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 21.529470, "sdRefIntergenicDistribution": 1.413352, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 51682, "distinctRankCount": 253, "maxRank": 20344.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 190252011, "mappedReadsCount": 143490748, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138796" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:1001568", "name": "pulmonary artery endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_arterial_pulmonary, Vascular", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 224.500414, "sdRefIntergenicDistribution": 1.255610, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 4711, "distinctRankCount": 46, "maxRank": 18375.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 190252011, "mappedReadsCount": 143490748, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138796" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000798", "name": "gamma-delta T cell" }, "cellTypeAuthorAnnotation": "gdT, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 11.744315, "sdRefIntergenicDistribution": 1.565837, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 101710, "distinctRankCount": 361, "maxRank": 21647.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 190252011, "mappedReadsCount": 143490748, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138796" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000990", "name": "conventional dendritic cell" }, "cellTypeAuthorAnnotation": "DC_1, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 72.038874, "sdRefIntergenicDistribution": 1.410114, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 15699, "distinctRankCount": 139, "maxRank": 18695.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 190252011, "mappedReadsCount": 143490748, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138796" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000990", "name": "conventional dendritic cell" }, "cellTypeAuthorAnnotation": "DC_2, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 23.414437, "sdRefIntergenicDistribution": 1.524972, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 50340, "distinctRankCount": 277, "maxRank": 20294.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 190252011, "mappedReadsCount": 143490748, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138796" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0002543", "name": "vein endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_venous_pulmonary, Vascular", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 169.645956, "sdRefIntergenicDistribution": 1.293682, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 6426, "distinctRankCount": 69, "maxRank": 18506.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 190252011, "mappedReadsCount": 143490748, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138796" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0002543", "name": "vein endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_venous_systemic, Vascular", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 938.967136, "sdRefIntergenicDistribution": 1.000000, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 0, "distinctRankCount": 0 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 190252011, "mappedReadsCount": 143490748, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138796" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000624", "name": "CD4-positive, alpha-beta T cell" }, "cellTypeAuthorAnnotation": "CD4_EM/Effector, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 8.811473, "sdRefIntergenicDistribution": 1.612872, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 139578, "distinctRankCount": 408, "maxRank": 22079.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 190252011, "mappedReadsCount": 143490748, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138796" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000624", "name": "CD4-positive, alpha-beta T cell" }, "cellTypeAuthorAnnotation": "CD4_naive/CM, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 26.144430, "sdRefIntergenicDistribution": 1.388529, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 41850, "distinctRankCount": 209, "maxRank": 20333.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 190252011, "mappedReadsCount": 143490748, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138796" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0002553", "name": "fibroblast of lung" }, "cellTypeAuthorAnnotation": "Fibro_adventitial, Stroma", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 14.608594, "sdRefIntergenicDistribution": 1.490134, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 80194, "distinctRankCount": 384, "maxRank": 21216.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 190252011, "mappedReadsCount": 143490748, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138796" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0002553", "name": "fibroblast of lung" }, "cellTypeAuthorAnnotation": "Fibro_alveolar, Stroma", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 80.319940, "sdRefIntergenicDistribution": 1.269070, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 13058, "distinctRankCount": 111, "maxRank": 19144.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 190252011, "mappedReadsCount": 143490748, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138796" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0002553", "name": "fibroblast of lung" }, "cellTypeAuthorAnnotation": "Fibro_immune_recruiting, Stroma", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 175.770501, "sdRefIntergenicDistribution": 1.343674, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 6315, "distinctRankCount": 73, "maxRank": 18442.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 190252011, "mappedReadsCount": 143490748, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138796" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000192", "name": "smooth muscle cell" }, "cellTypeAuthorAnnotation": "Muscle_smooth_pulmonary, Stroma", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 36.284137, "sdRefIntergenicDistribution": 1.445567, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 31683, "distinctRankCount": 185, "maxRank": 19752.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 190252011, "mappedReadsCount": 143490748, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138796" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000913", "name": "effector memory CD8-positive, alpha-beta T cell" }, "cellTypeAuthorAnnotation": "CD8_EM, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 27.613239, "sdRefIntergenicDistribution": 1.419686, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 39832, "distinctRankCount": 207, "maxRank": 20122.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 190252011, "mappedReadsCount": 143490748, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138796" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000913", "name": "effector memory CD8-positive, alpha-beta T cell" }, "cellTypeAuthorAnnotation": "CD8_EM/EMRA, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 31.467807, "sdRefIntergenicDistribution": 1.421487, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 35647, "distinctRankCount": 195, "maxRank": 19971.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 190252011, "mappedReadsCount": 143490748, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138796" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0002633", "name": "respiratory basal cell" }, "cellTypeAuthorAnnotation": "Basal, Epithelia", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 589.645737, "sdRefIntergenicDistribution": 1.299798, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1876, "distinctRankCount": 27, "maxRank": 17906.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 190252011, "mappedReadsCount": 143490748, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138796" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0001054", "name": "CD14-positive monocyte" }, "cellTypeAuthorAnnotation": "Monocyte_CD14, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 27.584652, "sdRefIntergenicDistribution": 1.602033, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 42634, "distinctRankCount": 228, "maxRank": 19951.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 190252011, "mappedReadsCount": 143490748, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138796" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000909", "name": "CD8-positive, alpha-beta memory T cell" }, "cellTypeAuthorAnnotation": "CD8_TRM, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 109.402922, "sdRefIntergenicDistribution": 1.276171, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 9508, "distinctRankCount": 96, "maxRank": 18802.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 190252011, "mappedReadsCount": 143490748, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138796" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000909", "name": "CD8-positive, alpha-beta memory T cell" }, "cellTypeAuthorAnnotation": "CD8_TRM/EM, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 32.230551, "sdRefIntergenicDistribution": 1.444754, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 34684, "distinctRankCount": 187, "maxRank": 19919.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 190252011, "mappedReadsCount": 143490748, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138796" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0002396", "name": "CD14-low, CD16-positive monocyte" }, "cellTypeAuthorAnnotation": "Monocyte_CD16, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 14.306922, "sdRefIntergenicDistribution": 1.617813, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 84963, "distinctRankCount": 335, "maxRank": 20715.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 190252011, "mappedReadsCount": 143490748, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138796" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000186", "name": "myofibroblast cell" }, "cellTypeAuthorAnnotation": "Fibro_myofibroblast, Stroma", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 63.252453, "sdRefIntergenicDistribution": 1.326649, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 17107, "distinctRankCount": 130, "maxRank": 19536.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 190252011, "mappedReadsCount": 143490748, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138796" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000235", "name": "macrophage" }, "cellTypeAuthorAnnotation": "Macro_AW_CX3CR1, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 1231.322249, "sdRefIntergenicDistribution": 1.512541, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 970, "distinctRankCount": 20, "maxRank": 17766.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 190252011, "mappedReadsCount": 143490748, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138796" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000623", "name": "natural killer cell" }, "cellTypeAuthorAnnotation": "NK_CD11d, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 111.640724, "sdRefIntergenicDistribution": 1.277611, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 9478, "distinctRankCount": 97, "maxRank": 18738.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 190252011, "mappedReadsCount": 143490748, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138796" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000623", "name": "natural killer cell" }, "cellTypeAuthorAnnotation": "NK_CD16hi, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 23.884564, "sdRefIntergenicDistribution": 1.449218, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 46463, "distinctRankCount": 248, "maxRank": 20662.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 190252011, "mappedReadsCount": 143490748, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138796" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000623", "name": "natural killer cell" }, "cellTypeAuthorAnnotation": "NK_CD56bright, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 89.642956, "sdRefIntergenicDistribution": 1.380825, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 11946, "distinctRankCount": 118, "maxRank": 19077.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 190252011, "mappedReadsCount": 143490748, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138796" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:1001603", "name": "lung macrophage" }, "cellTypeAuthorAnnotation": "Macro_CCL, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 371.187374, "sdRefIntergenicDistribution": 1.403847, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 2560, "distinctRankCount": 32, "maxRank": 18039.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 190252011, "mappedReadsCount": 143490748, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138796" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:1001603", "name": "lung macrophage" }, "cellTypeAuthorAnnotation": "Macro_CHIT1, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 35.773838, "sdRefIntergenicDistribution": 1.604852, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 35135, "distinctRankCount": 246, "maxRank": 19570.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 190252011, "mappedReadsCount": 143490748, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138796" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:1001603", "name": "lung macrophage" }, "cellTypeAuthorAnnotation": "Macro_dividing, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 162.866955, "sdRefIntergenicDistribution": 1.532590, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 7477, "distinctRankCount": 77, "maxRank": 18585.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 190252011, "mappedReadsCount": 143490748, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138796" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:1001603", "name": "lung macrophage" }, "cellTypeAuthorAnnotation": "Macro_intermediate, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 12.408541, "sdRefIntergenicDistribution": 1.615115, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 98897, "distinctRankCount": 417, "maxRank": 21171.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 190252011, "mappedReadsCount": 143490748, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138796" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:1001603", "name": "lung macrophage" }, "cellTypeAuthorAnnotation": "Macro_intravascular, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 24.869264, "sdRefIntergenicDistribution": 1.555873, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 47326, "distinctRankCount": 242, "maxRank": 20241.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 190252011, "mappedReadsCount": 143490748, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138796" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000897", "name": "CD4-positive, alpha-beta memory T cell" }, "cellTypeAuthorAnnotation": "CD4_TRM, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 24.418418, "sdRefIntergenicDistribution": 1.457696, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 46210, "distinctRankCount": 236, "maxRank": 20292.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 190252011, "mappedReadsCount": 143490748, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138796" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000077", "name": "mesothelial cell" }, "cellTypeAuthorAnnotation": "Mesothelia, Stroma", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 140.376441, "sdRefIntergenicDistribution": 1.575352, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 9580, "distinctRankCount": 92, "maxRank": 18692.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 190252011, "mappedReadsCount": 143490748, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138796" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000097", "name": "mast cell" }, "cellTypeAuthorAnnotation": "Mast_cell , Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 180.939395, "sdRefIntergenicDistribution": 1.378626, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 5374, "distinctRankCount": 57, "maxRank": 18398.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 190252011, "mappedReadsCount": 143490748, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138796" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000940", "name": "mucosal invariant T cell" }, "cellTypeAuthorAnnotation": "MAIT, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 92.767518, "sdRefIntergenicDistribution": 1.326282, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 11415, "distinctRankCount": 103, "maxRank": 18851.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 190252011, "mappedReadsCount": 143490748, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138796" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0002063", "name": "type II pneumocyte" }, "cellTypeAuthorAnnotation": "AT2, Epithelia", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 2.212969, "sdRefIntergenicDistribution": 1.904999, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 705100, "distinctRankCount": 887, "maxRank": 23998.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 190252011, "mappedReadsCount": 143490748, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138796" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000987", "name": "IgA plasma cell" }, "cellTypeAuthorAnnotation": "B_plasma_IgA, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 17.910987, "sdRefIntergenicDistribution": 1.527415, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 65456, "distinctRankCount": 242, "maxRank": 19863.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 190252011, "mappedReadsCount": 143490748, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138796" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000158", "name": "club cell" }, "cellTypeAuthorAnnotation": "Secretory_Club, Epithelia", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 245.614583, "sdRefIntergenicDistribution": 1.537183, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 4916, "distinctRankCount": 52, "maxRank": 18110.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 190252011, "mappedReadsCount": 143490748, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138796" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000787", "name": "memory B cell" }, "cellTypeAuthorAnnotation": "B_memory, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 31.328756, "sdRefIntergenicDistribution": 1.380672, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 35331, "distinctRankCount": 192, "maxRank": 19514.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 190252011, "mappedReadsCount": 143490748, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138796" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000784", "name": "plasmacytoid dendritic cell" }, "cellTypeAuthorAnnotation": "DC_plasmacytoid, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 406.794293, "sdRefIntergenicDistribution": 1.311272, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 2462, "distinctRankCount": 38, "maxRank": 18071.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 190252011, "mappedReadsCount": 143490748, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138796" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0009115", "name": "lymph node lymphatic vessel endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_Lymphatic, Vascular", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 102.360487, "sdRefIntergenicDistribution": 1.384322, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 11362, "distinctRankCount": 110, "maxRank": 18692.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 190252011, "mappedReadsCount": 143490748, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138796" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000985", "name": "IgG plasma cell" }, "cellTypeAuthorAnnotation": "B_plasma_IgG, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 28.088914, "sdRefIntergenicDistribution": 1.495002, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 40834, "distinctRankCount": 161, "maxRank": 19241.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 190252011, "mappedReadsCount": 143490748, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138796" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000815", "name": "regulatory T cell" }, "cellTypeAuthorAnnotation": "T_reg, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 103.448193, "sdRefIntergenicDistribution": 1.375844, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 10687, "distinctRankCount": 99, "maxRank": 18726.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 190252011, "mappedReadsCount": 143490748, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138796" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0001065", "name": "innate lymphoid cell" }, "cellTypeAuthorAnnotation": "ILC, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 142.293674, "sdRefIntergenicDistribution": 1.293894, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 7332, "distinctRankCount": 83, "maxRank": 18530.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 190252011, "mappedReadsCount": 143490748, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138796" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000788", "name": "naive B cell" }, "cellTypeAuthorAnnotation": "B_naive, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 369.103861, "sdRefIntergenicDistribution": 1.260593, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 2841, "distinctRankCount": 46, "maxRank": 17955.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 190252011, "mappedReadsCount": 143490748, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138796" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000980", "name": "plasmablast" }, "cellTypeAuthorAnnotation": "B_plasmablast, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 698.129336, "sdRefIntergenicDistribution": 1.198157, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1364, "distinctRankCount": 27, "maxRank": 17842.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 168886031, "mappedReadsCount": 103038437, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138809" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000913", "name": "effector memory CD8-positive, alpha-beta T cell" }, "cellTypeAuthorAnnotation": "CD8_EM, Immune", "devStage": { "id": "HsapDv:0000123", "name": "29-year-old stage (human)" }, "devStageAuthorAnnotation": "25-30 (29 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 77.669191, "sdRefIntergenicDistribution": 1.354152, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 13098, "distinctRankCount": 134, "maxRank": 18879.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 168886031, "mappedReadsCount": 103038437, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138809" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000913", "name": "effector memory CD8-positive, alpha-beta T cell" }, "cellTypeAuthorAnnotation": "CD8_EM/EMRA, Immune", "devStage": { "id": "HsapDv:0000123", "name": "29-year-old stage (human)" }, "devStageAuthorAnnotation": "25-30 (29 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 55.819632, "sdRefIntergenicDistribution": 1.386022, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 19276, "distinctRankCount": 146, "maxRank": 19116.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 168886031, "mappedReadsCount": 103038437, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138809" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000583", "name": "alveolar macrophage" }, "cellTypeAuthorAnnotation": "Macro_alveolar, Immune", "devStage": { "id": "HsapDv:0000123", "name": "29-year-old stage (human)" }, "devStageAuthorAnnotation": "25-30 (29 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 21.176247, "sdRefIntergenicDistribution": 1.744159, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 56832, "distinctRankCount": 328, "maxRank": 20537.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 168886031, "mappedReadsCount": 103038437, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138809" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000583", "name": "alveolar macrophage" }, "cellTypeAuthorAnnotation": "Macro_alveolar_metallothioneins, Immune", "devStage": { "id": "HsapDv:0000123", "name": "29-year-old stage (human)" }, "devStageAuthorAnnotation": "25-30 (29 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 664.923935, "sdRefIntergenicDistribution": 1.294931, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1506, "distinctRankCount": 26, "maxRank": 17829.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 168886031, "mappedReadsCount": 103038437, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138809" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0002553", "name": "fibroblast of lung" }, "cellTypeAuthorAnnotation": "Fibro_adventitial, Stroma", "devStage": { "id": "HsapDv:0000123", "name": "29-year-old stage (human)" }, "devStageAuthorAnnotation": "25-30 (29 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 493.339916, "sdRefIntergenicDistribution": 1.000000, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 0, "distinctRankCount": 0 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 168886031, "mappedReadsCount": 103038437, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138809" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0001054", "name": "CD14-positive monocyte" }, "cellTypeAuthorAnnotation": "Monocyte_CD14, Immune", "devStage": { "id": "HsapDv:0000123", "name": "29-year-old stage (human)" }, "devStageAuthorAnnotation": "25-30 (29 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 20.408763, "sdRefIntergenicDistribution": 1.536500, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 56027, "distinctRankCount": 293, "maxRank": 20410.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 168886031, "mappedReadsCount": 103038437, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138809" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0009115", "name": "lymph node lymphatic vessel endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_Lymphatic, Vascular", "devStage": { "id": "HsapDv:0000123", "name": "29-year-old stage (human)" }, "devStageAuthorAnnotation": "25-30 (29 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 43.786430, "sdRefIntergenicDistribution": 1.382156, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 24845, "distinctRankCount": 236, "maxRank": 19658.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 168886031, "mappedReadsCount": 103038437, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138809" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:1001568", "name": "pulmonary artery endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_arterial_pulmonary, Vascular", "devStage": { "id": "HsapDv:0000123", "name": "29-year-old stage (human)" }, "devStageAuthorAnnotation": "25-30 (29 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 325.337703, "sdRefIntergenicDistribution": 1.322767, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 3278, "distinctRankCount": 53, "maxRank": 18061.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 168886031, "mappedReadsCount": 103038437, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138809" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000814", "name": "mature NK T cell" }, "cellTypeAuthorAnnotation": "NKT, Immune", "devStage": { "id": "HsapDv:0000123", "name": "29-year-old stage (human)" }, "devStageAuthorAnnotation": "25-30 (29 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 51.172468, "sdRefIntergenicDistribution": 1.373568, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 20744, "distinctRankCount": 184, "maxRank": 19278.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 168886031, "mappedReadsCount": 103038437, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138809" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0002633", "name": "respiratory basal cell" }, "cellTypeAuthorAnnotation": "Dividing_Basal, Epithelia", "devStage": { "id": "HsapDv:0000123", "name": "29-year-old stage (human)" }, "devStageAuthorAnnotation": "25-30 (29 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 478.746546, "sdRefIntergenicDistribution": 1.354802, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1933, "distinctRankCount": 29, "maxRank": 17943.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 168886031, "mappedReadsCount": 103038437, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138809" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:1001603", "name": "lung macrophage" }, "cellTypeAuthorAnnotation": "Macro_CHIT1, Immune", "devStage": { "id": "HsapDv:0000123", "name": "29-year-old stage (human)" }, "devStageAuthorAnnotation": "25-30 (29 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 23.999430, "sdRefIntergenicDistribution": 1.514968, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 49385, "distinctRankCount": 344, "maxRank": 19901.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 168886031, "mappedReadsCount": 103038437, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138809" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:1001603", "name": "lung macrophage" }, "cellTypeAuthorAnnotation": "Macro_intermediate, Immune", "devStage": { "id": "HsapDv:0000123", "name": "29-year-old stage (human)" }, "devStageAuthorAnnotation": "25-30 (29 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 166.362687, "sdRefIntergenicDistribution": 1.397891, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 6530, "distinctRankCount": 86, "maxRank": 18232.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 168886031, "mappedReadsCount": 103038437, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138809" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:1001603", "name": "lung macrophage" }, "cellTypeAuthorAnnotation": "Macro_intravascular, Immune", "devStage": { "id": "HsapDv:0000123", "name": "29-year-old stage (human)" }, "devStageAuthorAnnotation": "25-30 (29 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 30.600001, "sdRefIntergenicDistribution": 1.560071, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 37785, "distinctRankCount": 298, "maxRank": 19948.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 168886031, "mappedReadsCount": 103038437, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138809" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000624", "name": "CD4-positive, alpha-beta T cell" }, "cellTypeAuthorAnnotation": "CD4_EM/Effector, Immune", "devStage": { "id": "HsapDv:0000123", "name": "29-year-old stage (human)" }, "devStageAuthorAnnotation": "25-30 (29 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 61.819096, "sdRefIntergenicDistribution": 1.416879, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 17110, "distinctRankCount": 159, "maxRank": 19069.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 168886031, "mappedReadsCount": 103038437, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138809" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000624", "name": "CD4-positive, alpha-beta T cell" }, "cellTypeAuthorAnnotation": "CD4_naive/CM, Immune", "devStage": { "id": "HsapDv:0000123", "name": "29-year-old stage (human)" }, "devStageAuthorAnnotation": "25-30 (29 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 171.595008, "sdRefIntergenicDistribution": 1.394764, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 6131, "distinctRankCount": 65, "maxRank": 18204.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 168886031, "mappedReadsCount": 103038437, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138809" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000987", "name": "IgA plasma cell" }, "cellTypeAuthorAnnotation": "B_plasma_IgA, Immune", "devStage": { "id": "HsapDv:0000123", "name": "29-year-old stage (human)" }, "devStageAuthorAnnotation": "25-30 (29 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 26.514455, "sdRefIntergenicDistribution": 1.576816, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 44574, "distinctRankCount": 142, "maxRank": 18892.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 168886031, "mappedReadsCount": 103038437, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138809" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000897", "name": "CD4-positive, alpha-beta memory T cell" }, "cellTypeAuthorAnnotation": "CD4_TRM, Immune", "devStage": { "id": "HsapDv:0000123", "name": "29-year-old stage (human)" }, "devStageAuthorAnnotation": "25-30 (29 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 220.024816, "sdRefIntergenicDistribution": 1.296957, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 4648, "distinctRankCount": 60, "maxRank": 18175.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 168886031, "mappedReadsCount": 103038437, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138809" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000784", "name": "plasmacytoid dendritic cell" }, "cellTypeAuthorAnnotation": "DC_plasmacytoid, Immune", "devStage": { "id": "HsapDv:0000123", "name": "29-year-old stage (human)" }, "devStageAuthorAnnotation": "25-30 (29 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 807.349428, "sdRefIntergenicDistribution": 1.349707, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1256, "distinctRankCount": 25, "maxRank": 17805.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 168886031, "mappedReadsCount": 103038437, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138809" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000909", "name": "CD8-positive, alpha-beta memory T cell" }, "cellTypeAuthorAnnotation": "CD8_TRM, Immune", "devStage": { "id": "HsapDv:0000123", "name": "29-year-old stage (human)" }, "devStageAuthorAnnotation": "25-30 (29 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 606.740124, "sdRefIntergenicDistribution": 1.312295, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1673, "distinctRankCount": 25, "maxRank": 17851.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 168886031, "mappedReadsCount": 103038437, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138809" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000909", "name": "CD8-positive, alpha-beta memory T cell" }, "cellTypeAuthorAnnotation": "CD8_TRM/EM, Immune", "devStage": { "id": "HsapDv:0000123", "name": "29-year-old stage (human)" }, "devStageAuthorAnnotation": "25-30 (29 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 119.249233, "sdRefIntergenicDistribution": 1.288670, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 8796, "distinctRankCount": 113, "maxRank": 18462.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 168886031, "mappedReadsCount": 103038437, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138809" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0002144", "name": "capillary endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_Cap_g, Vascular", "devStage": { "id": "HsapDv:0000123", "name": "29-year-old stage (human)" }, "devStageAuthorAnnotation": "25-30 (29 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 231.827534, "sdRefIntergenicDistribution": 1.340344, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 4430, "distinctRankCount": 49, "maxRank": 18232.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 168886031, "mappedReadsCount": 103038437, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138809" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000232", "name": "erythrocyte" }, "cellTypeAuthorAnnotation": "Erythrocyte, Vascular", "devStage": { "id": "HsapDv:0000123", "name": "29-year-old stage (human)" }, "devStageAuthorAnnotation": "25-30 (29 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 443.657286, "sdRefIntergenicDistribution": 1.295515, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 2277, "distinctRankCount": 36, "maxRank": 17966.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 168886031, "mappedReadsCount": 103038437, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138809" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000990", "name": "conventional dendritic cell" }, "cellTypeAuthorAnnotation": "DC_1, Immune", "devStage": { "id": "HsapDv:0000123", "name": "29-year-old stage (human)" }, "devStageAuthorAnnotation": "25-30 (29 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 129.542445, "sdRefIntergenicDistribution": 1.326760, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 8070, "distinctRankCount": 103, "maxRank": 18349.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 168886031, "mappedReadsCount": 103038437, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138809" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000990", "name": "conventional dendritic cell" }, "cellTypeAuthorAnnotation": "DC_2, Immune", "devStage": { "id": "HsapDv:0000123", "name": "29-year-old stage (human)" }, "devStageAuthorAnnotation": "25-30 (29 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 23.230723, "sdRefIntergenicDistribution": 1.492598, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 49837, "distinctRankCount": 341, "maxRank": 20130.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 168886031, "mappedReadsCount": 103038437, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138809" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0002543", "name": "vein endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_venous_pulmonary, Vascular", "devStage": { "id": "HsapDv:0000123", "name": "29-year-old stage (human)" }, "devStageAuthorAnnotation": "25-30 (29 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 622.039165, "sdRefIntergenicDistribution": 1.287182, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1642, "distinctRankCount": 29, "maxRank": 17813.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 168886031, "mappedReadsCount": 103038437, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138809" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0002543", "name": "vein endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_venous_systemic, Vascular", "devStage": { "id": "HsapDv:0000123", "name": "29-year-old stage (human)" }, "devStageAuthorAnnotation": "25-30 (29 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 1337.690808, "sdRefIntergenicDistribution": 1.378319, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 878, "distinctRankCount": 19, "maxRank": 17742.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 168886031, "mappedReadsCount": 103038437, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138809" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000788", "name": "naive B cell" }, "cellTypeAuthorAnnotation": "B_naive, Immune", "devStage": { "id": "HsapDv:0000123", "name": "29-year-old stage (human)" }, "devStageAuthorAnnotation": "25-30 (29 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 397.809403, "sdRefIntergenicDistribution": 1.409579, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 2658, "distinctRankCount": 52, "maxRank": 17932.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 168886031, "mappedReadsCount": 103038437, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138809" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000160", "name": "goblet cell" }, "cellTypeAuthorAnnotation": "Secretory_Goblet, Epithelia", "devStage": { "id": "HsapDv:0000123", "name": "29-year-old stage (human)" }, "devStageAuthorAnnotation": "25-30 (29 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 54.819238, "sdRefIntergenicDistribution": 1.665370, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 22035, "distinctRankCount": 193, "maxRank": 19370.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 168886031, "mappedReadsCount": 103038437, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138809" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000235", "name": "macrophage" }, "cellTypeAuthorAnnotation": "Macro_AW_CX3CR1, Immune", "devStage": { "id": "HsapDv:0000123", "name": "29-year-old stage (human)" }, "devStageAuthorAnnotation": "25-30 (29 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 113.528816, "sdRefIntergenicDistribution": 1.365988, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 9407, "distinctRankCount": 95, "maxRank": 18556.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 168886031, "mappedReadsCount": 103038437, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138809" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000787", "name": "memory B cell" }, "cellTypeAuthorAnnotation": "B_memory, Immune", "devStage": { "id": "HsapDv:0000123", "name": "29-year-old stage (human)" }, "devStageAuthorAnnotation": "25-30 (29 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 176.439321, "sdRefIntergenicDistribution": 1.320515, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 5817, "distinctRankCount": 83, "maxRank": 18105.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 168886031, "mappedReadsCount": 103038437, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138809" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000798", "name": "gamma-delta T cell" }, "cellTypeAuthorAnnotation": "gdT, Immune", "devStage": { "id": "HsapDv:0000123", "name": "29-year-old stage (human)" }, "devStageAuthorAnnotation": "25-30 (29 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 222.551464, "sdRefIntergenicDistribution": 1.319686, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 4569, "distinctRankCount": 62, "maxRank": 18134.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 168886031, "mappedReadsCount": 103038437, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138809" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000623", "name": "natural killer cell" }, "cellTypeAuthorAnnotation": "NK_CD11d, Immune", "devStage": { "id": "HsapDv:0000123", "name": "29-year-old stage (human)" }, "devStageAuthorAnnotation": "25-30 (29 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 536.908170, "sdRefIntergenicDistribution": 1.259454, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1922, "distinctRankCount": 23, "maxRank": 17906.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 168886031, "mappedReadsCount": 103038437, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138809" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000623", "name": "natural killer cell" }, "cellTypeAuthorAnnotation": "NK_CD16hi, Immune", "devStage": { "id": "HsapDv:0000123", "name": "29-year-old stage (human)" }, "devStageAuthorAnnotation": "25-30 (29 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 23.413522, "sdRefIntergenicDistribution": 1.457346, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 47407, "distinctRankCount": 279, "maxRank": 20455.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 168886031, "mappedReadsCount": 103038437, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138809" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0002368", "name": "respiratory epithelial cell" }, "cellTypeAuthorAnnotation": "Suprabasal, Epithelia", "devStage": { "id": "HsapDv:0000123", "name": "29-year-old stage (human)" }, "devStageAuthorAnnotation": "25-30 (29 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 129.342207, "sdRefIntergenicDistribution": 1.388407, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 8382, "distinctRankCount": 83, "maxRank": 18510.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 168886031, "mappedReadsCount": 103038437, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138809" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000097", "name": "mast cell" }, "cellTypeAuthorAnnotation": "Mast_cell , Immune", "devStage": { "id": "HsapDv:0000123", "name": "29-year-old stage (human)" }, "devStageAuthorAnnotation": "25-30 (29 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 61.472048, "sdRefIntergenicDistribution": 1.490229, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 18258, "distinctRankCount": 135, "maxRank": 19015.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 168886031, "mappedReadsCount": 103038437, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138809" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0002396", "name": "CD14-low, CD16-positive monocyte" }, "cellTypeAuthorAnnotation": "Monocyte_CD16, Immune", "devStage": { "id": "HsapDv:0000123", "name": "29-year-old stage (human)" }, "devStageAuthorAnnotation": "25-30 (29 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 14.713534, "sdRefIntergenicDistribution": 1.607257, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 81521, "distinctRankCount": 484, "maxRank": 20918.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 192728338, "mappedReadsCount": 125732144, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138812" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0002144", "name": "capillary endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_Cap_a, Vascular", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 8.008912, "sdRefIntergenicDistribution": 1.704235, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 163537, "distinctRankCount": 408, "maxRank": 22976.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 192728338, "mappedReadsCount": 125732144, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138812" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0002144", "name": "capillary endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_Cap_g, Vascular", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 23.381434, "sdRefIntergenicDistribution": 1.486271, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 46286, "distinctRankCount": 199, "maxRank": 21275.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 192728338, "mappedReadsCount": 125732144, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138812" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0001054", "name": "CD14-positive monocyte" }, "cellTypeAuthorAnnotation": "Monocyte_CD14, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 274.158854, "sdRefIntergenicDistribution": 1.209909, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 3715, "distinctRankCount": 39, "maxRank": 18178.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 192728338, "mappedReadsCount": 125732144, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138812" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0002396", "name": "CD14-low, CD16-positive monocyte" }, "cellTypeAuthorAnnotation": "Monocyte_CD16, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 91.432247, "sdRefIntergenicDistribution": 1.316626, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 11630, "distinctRankCount": 112, "maxRank": 18892.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 192728338, "mappedReadsCount": 125732144, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138812" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0002543", "name": "vein endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_venous_pulmonary, Vascular", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 128.865426, "sdRefIntergenicDistribution": 1.273031, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 7878, "distinctRankCount": 59, "maxRank": 18876.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 192728338, "mappedReadsCount": 125732144, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138812" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0002543", "name": "vein endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_venous_systemic, Vascular", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 103.279145, "sdRefIntergenicDistribution": 1.272605, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 9251, "distinctRankCount": 64, "maxRank": 19086.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 192728338, "mappedReadsCount": 125732144, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138812" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0002553", "name": "fibroblast of lung" }, "cellTypeAuthorAnnotation": "Fibro_adventitial, Stroma", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 1.558213, "sdRefIntergenicDistribution": 2.419404, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1865360, "distinctRankCount": 1998, "maxRank": 25632.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 192728338, "mappedReadsCount": 125732144, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138812" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0002553", "name": "fibroblast of lung" }, "cellTypeAuthorAnnotation": "Fibro_alveolar, Stroma", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 4.754472, "sdRefIntergenicDistribution": 1.662401, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 277702, "distinctRankCount": 621, "maxRank": 23562.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 192728338, "mappedReadsCount": 125732144, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138812" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000623", "name": "natural killer cell" }, "cellTypeAuthorAnnotation": "NK_CD11d, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 198.219535, "sdRefIntergenicDistribution": 1.244560, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 5101, "distinctRankCount": 55, "maxRank": 18437.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 192728338, "mappedReadsCount": 125732144, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138812" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000623", "name": "natural killer cell" }, "cellTypeAuthorAnnotation": "NK_CD16hi, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 21.517622, "sdRefIntergenicDistribution": 1.415320, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 50601, "distinctRankCount": 256, "maxRank": 20919.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 192728338, "mappedReadsCount": 125732144, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138812" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000623", "name": "natural killer cell" }, "cellTypeAuthorAnnotation": "NK_CD56bright, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 205.024196, "sdRefIntergenicDistribution": 1.251335, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 4699, "distinctRankCount": 61, "maxRank": 18358.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 192728338, "mappedReadsCount": 125732144, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138812" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000990", "name": "conventional dendritic cell" }, "cellTypeAuthorAnnotation": "DC_1, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 74.543554, "sdRefIntergenicDistribution": 1.299361, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 14266, "distinctRankCount": 134, "maxRank": 18757.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 192728338, "mappedReadsCount": 125732144, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138812" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:1001603", "name": "lung macrophage" }, "cellTypeAuthorAnnotation": "Macro_CHIT1, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 51.457860, "sdRefIntergenicDistribution": 1.389015, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 20916, "distinctRankCount": 152, "maxRank": 19543.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 192728338, "mappedReadsCount": 125732144, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138812" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:1001603", "name": "lung macrophage" }, "cellTypeAuthorAnnotation": "Macro_intravascular, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 62.831836, "sdRefIntergenicDistribution": 1.330194, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 16252, "distinctRankCount": 148, "maxRank": 19390.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 192728338, "mappedReadsCount": 125732144, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138812" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000158", "name": "club cell" }, "cellTypeAuthorAnnotation": "Secretory_Club, Epithelia", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 5.265019, "sdRefIntergenicDistribution": 1.688800, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 249732, "distinctRankCount": 534, "maxRank": 22984.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 192728338, "mappedReadsCount": 125732144, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138812" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000097", "name": "mast cell" }, "cellTypeAuthorAnnotation": "Mast_cell , Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 1404.081124, "sdRefIntergenicDistribution": 1.155498, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 697, "distinctRankCount": 16, "maxRank": 17750.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 192728338, "mappedReadsCount": 125732144, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138812" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000814", "name": "mature NK T cell" }, "cellTypeAuthorAnnotation": "NKT, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 92.746970, "sdRefIntergenicDistribution": 1.243424, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 10706, "distinctRankCount": 93, "maxRank": 19000.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 192728338, "mappedReadsCount": 125732144, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138812" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0002633", "name": "respiratory basal cell" }, "cellTypeAuthorAnnotation": "Basal, Epithelia", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 3.696687, "sdRefIntergenicDistribution": 1.779646, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 390502, "distinctRankCount": 1086, "maxRank": 24342.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 192728338, "mappedReadsCount": 125732144, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138812" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0002633", "name": "respiratory basal cell" }, "cellTypeAuthorAnnotation": "Dividing_Basal, Epithelia", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 6.904731, "sdRefIntergenicDistribution": 1.557706, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 178858, "distinctRankCount": 750, "maxRank": 22997.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 192728338, "mappedReadsCount": 125732144, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138812" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000624", "name": "CD4-positive, alpha-beta T cell" }, "cellTypeAuthorAnnotation": "CD4_EM/Effector, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 79.869084, "sdRefIntergenicDistribution": 1.315022, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 12164, "distinctRankCount": 114, "maxRank": 19150.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 192728338, "mappedReadsCount": 125732144, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138812" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000897", "name": "CD4-positive, alpha-beta memory T cell" }, "cellTypeAuthorAnnotation": "CD4_TRM, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 47.343586, "sdRefIntergenicDistribution": 1.378225, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 22098, "distinctRankCount": 163, "maxRank": 19810.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 192728338, "mappedReadsCount": 125732144, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138812" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0019018", "name": "blood vessel smooth muscle cell" }, "cellTypeAuthorAnnotation": "Muscle_smooth_arterial_systemic, Stroma", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 91.818266, "sdRefIntergenicDistribution": 1.225603, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 11260, "distinctRankCount": 100, "maxRank": 18880.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 192728338, "mappedReadsCount": 125732144, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138812" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000186", "name": "myofibroblast cell" }, "cellTypeAuthorAnnotation": "Fibro_myofibroblast, Stroma", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 9.857594, "sdRefIntergenicDistribution": 1.557337, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 122111, "distinctRankCount": 449, "maxRank": 22535.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 192728338, "mappedReadsCount": 125732144, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138812" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000583", "name": "alveolar macrophage" }, "cellTypeAuthorAnnotation": "Macro_alveolar, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 33.213433, "sdRefIntergenicDistribution": 1.394790, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 33505, "distinctRankCount": 211, "maxRank": 19853.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 192728338, "mappedReadsCount": 125732144, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138812" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000160", "name": "goblet cell" }, "cellTypeAuthorAnnotation": "Secretory_Goblet, Epithelia", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 1.478404, "sdRefIntergenicDistribution": 2.163119, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1404146, "distinctRankCount": 1875, "maxRank": 25126.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 192728338, "mappedReadsCount": 125732144, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138812" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0001065", "name": "innate lymphoid cell" }, "cellTypeAuthorAnnotation": "ILC, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 28.243975, "sdRefIntergenicDistribution": 1.363159, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 37366, "distinctRankCount": 239, "maxRank": 20460.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 192728338, "mappedReadsCount": 125732144, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138812" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000192", "name": "smooth muscle cell" }, "cellTypeAuthorAnnotation": "Muscle_smooth_pulmonary, Stroma", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 26.671701, "sdRefIntergenicDistribution": 1.349254, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 41060, "distinctRankCount": 209, "maxRank": 20318.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 192728338, "mappedReadsCount": 125732144, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138812" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:1001568", "name": "pulmonary artery endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_arterial_pulmonary, Vascular", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 60.211183, "sdRefIntergenicDistribution": 1.296586, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 17006, "distinctRankCount": 129, "maxRank": 19625.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 192728338, "mappedReadsCount": 125732144, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138812" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000787", "name": "memory B cell" }, "cellTypeAuthorAnnotation": "B_memory, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 163.127304, "sdRefIntergenicDistribution": 1.265964, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 6313, "distinctRankCount": 72, "maxRank": 18385.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 192728338, "mappedReadsCount": 125732144, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138812" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000913", "name": "effector memory CD8-positive, alpha-beta T cell" }, "cellTypeAuthorAnnotation": "CD8_EM, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 438.212076, "sdRefIntergenicDistribution": 1.254532, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 2214, "distinctRankCount": 32, "maxRank": 18002.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 192728338, "mappedReadsCount": 125732144, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138812" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000913", "name": "effector memory CD8-positive, alpha-beta T cell" }, "cellTypeAuthorAnnotation": "CD8_EM/EMRA, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 82.415422, "sdRefIntergenicDistribution": 1.300207, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 12438, "distinctRankCount": 106, "maxRank": 19031.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 192728338, "mappedReadsCount": 125732144, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138812" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000985", "name": "IgG plasma cell" }, "cellTypeAuthorAnnotation": "B_plasma_IgG, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 21.729768, "sdRefIntergenicDistribution": 1.608946, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 53019, "distinctRankCount": 155, "maxRank": 19219.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 192728338, "mappedReadsCount": 125732144, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138812" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000987", "name": "IgA plasma cell" }, "cellTypeAuthorAnnotation": "B_plasma_IgA, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 18.339068, "sdRefIntergenicDistribution": 1.527438, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 62624, "distinctRankCount": 163, "maxRank": 19525.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 192728338, "mappedReadsCount": 125732144, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138812" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0009115", "name": "lymph node lymphatic vessel endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_Lymphatic, Vascular", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 4.264951, "sdRefIntergenicDistribution": 1.852697, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 365069, "distinctRankCount": 828, "maxRank": 24037.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 192728338, "mappedReadsCount": 125732144, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138812" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0002368", "name": "respiratory epithelial cell" }, "cellTypeAuthorAnnotation": "Suprabasal, Epithelia", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 4.356733, "sdRefIntergenicDistribution": 1.676489, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 307765, "distinctRankCount": 854, "maxRank": 23499.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 192728338, "mappedReadsCount": 125732144, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138812" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000067", "name": "ciliated epithelial cell" }, "cellTypeAuthorAnnotation": "Ciliated, Epithelia", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 1.638071, "sdRefIntergenicDistribution": 3.189179, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 5578119, "distinctRankCount": 5865, "maxRank": 27243.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 192728338, "mappedReadsCount": 125732144, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138812" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0009089", "name": "lung pericyte" }, "cellTypeAuthorAnnotation": "Muscle_pericyte_pulmonary, Stroma", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 327.940697, "sdRefIntergenicDistribution": 1.248892, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 2872, "distinctRankCount": 30, "maxRank": 18257.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 192728338, "mappedReadsCount": 125732144, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138812" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:1000413", "name": "endothelial cell of artery" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_arterial_systemic, Vascular", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 42.405969, "sdRefIntergenicDistribution": 1.362090, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 24899, "distinctRankCount": 177, "maxRank": 20001.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 192728338, "mappedReadsCount": 125732144, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138812" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000669", "name": "pericyte cell" }, "cellTypeAuthorAnnotation": "Muscle_pericyte_systemic, Stroma", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 319.965249, "sdRefIntergenicDistribution": 1.256753, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 3541, "distinctRankCount": 45, "maxRank": 18207.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 192728338, "mappedReadsCount": 125732144, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138812" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000077", "name": "mesothelial cell" }, "cellTypeAuthorAnnotation": "Mesothelia, Stroma", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 52.081826, "sdRefIntergenicDistribution": 1.333696, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 20123, "distinctRankCount": 153, "maxRank": 19902.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 192728338, "mappedReadsCount": 125732144, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138812" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000798", "name": "gamma-delta T cell" }, "cellTypeAuthorAnnotation": "gdT, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 241.405609, "sdRefIntergenicDistribution": 1.261613, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 4116, "distinctRankCount": 57, "maxRank": 18213.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 192728338, "mappedReadsCount": 125732144, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138812" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000146", "name": "simple columnar epithelial cell" }, "cellTypeAuthorAnnotation": "SMG_Duct, Epithelia", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 17.323734, "sdRefIntergenicDistribution": 1.513878, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 71297, "distinctRankCount": 400, "maxRank": 20812.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 192728338, "mappedReadsCount": 125732144, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138812" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0017000", "name": "pulmonary ionocyte" }, "cellTypeAuthorAnnotation": "Ionocyte_n_Brush, Epithelia", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 118.097314, "sdRefIntergenicDistribution": 1.288605, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 8792, "distinctRankCount": 99, "maxRank": 19028.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 192728338, "mappedReadsCount": 125732144, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138812" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:4033044", "name": "deuterosomal cell" }, "cellTypeAuthorAnnotation": "Deuterosomal, Epithelia", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 13.568655, "sdRefIntergenicDistribution": 1.627380, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 91245, "distinctRankCount": 636, "maxRank": 22134.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 192728338, "mappedReadsCount": 125732144, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138812" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000319", "name": "mucus secreting cell" }, "cellTypeAuthorAnnotation": "SMG_Mucous, Epithelia", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 373.439513, "sdRefIntergenicDistribution": 1.333619, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 3127, "distinctRankCount": 46, "maxRank": 17992.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 192728338, "mappedReadsCount": 125732144, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138812" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0019001", "name": "tracheobronchial serous cell" }, "cellTypeAuthorAnnotation": "SMG_Serous, Epithelia", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 1240.892434, "sdRefIntergenicDistribution": 1.717766, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1080, "distinctRankCount": 19, "maxRank": 17758.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 170339242, "mappedReadsCount": 115195054, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138818" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0002144", "name": "capillary endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_Cap_a, Vascular", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 1132.858508, "sdRefIntergenicDistribution": 1.211568, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 748, "distinctRankCount": 14, "maxRank": 17793.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 170339242, "mappedReadsCount": 115195054, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138818" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0002144", "name": "capillary endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_Cap_g, Vascular", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 263.106281, "sdRefIntergenicDistribution": 1.128257, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 3786, "distinctRankCount": 38, "maxRank": 18324.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 170339242, "mappedReadsCount": 115195054, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138818" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000583", "name": "alveolar macrophage" }, "cellTypeAuthorAnnotation": "Macro_alveolar, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 2.888141, "sdRefIntergenicDistribution": 1.642159, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 458023, "distinctRankCount": 905, "maxRank": 22895.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 170339242, "mappedReadsCount": 115195054, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138818" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0002062", "name": "type I pneumocyte" }, "cellTypeAuthorAnnotation": "AT1 , Epithelia", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 65.265808, "sdRefIntergenicDistribution": 1.349844, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 16882, "distinctRankCount": 140, "maxRank": 19228.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 170339242, "mappedReadsCount": 115195054, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138818" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000814", "name": "mature NK T cell" }, "cellTypeAuthorAnnotation": "NKT, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 4.216663, "sdRefIntergenicDistribution": 1.838546, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 353171, "distinctRankCount": 631, "maxRank": 23055.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 170339242, "mappedReadsCount": 115195054, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138818" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:1001568", "name": "pulmonary artery endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_arterial_pulmonary, Vascular", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 16.982553, "sdRefIntergenicDistribution": 1.696358, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 75741, "distinctRankCount": 534, "maxRank": 21275.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 170339242, "mappedReadsCount": 115195054, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138818" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0009089", "name": "lung pericyte" }, "cellTypeAuthorAnnotation": "Muscle_pericyte_pulmonary, Stroma", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 448.262813, "sdRefIntergenicDistribution": 1.246479, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 2308, "distinctRankCount": 30, "maxRank": 18083.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 170339242, "mappedReadsCount": 115195054, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138818" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000798", "name": "gamma-delta T cell" }, "cellTypeAuthorAnnotation": "gdT, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 6.843861, "sdRefIntergenicDistribution": 1.762643, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 195742, "distinctRankCount": 473, "maxRank": 22581.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 170339242, "mappedReadsCount": 115195054, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138818" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000990", "name": "conventional dendritic cell" }, "cellTypeAuthorAnnotation": "DC_1, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 112.451445, "sdRefIntergenicDistribution": 1.482026, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 9814, "distinctRankCount": 97, "maxRank": 18431.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 170339242, "mappedReadsCount": 115195054, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138818" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000990", "name": "conventional dendritic cell" }, "cellTypeAuthorAnnotation": "DC_2, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 36.625370, "sdRefIntergenicDistribution": 1.430537, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 30420, "distinctRankCount": 188, "maxRank": 19717.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 170339242, "mappedReadsCount": 115195054, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138818" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0002543", "name": "vein endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_venous_pulmonary, Vascular", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 79.616111, "sdRefIntergenicDistribution": 1.205389, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 13121, "distinctRankCount": 110, "maxRank": 19054.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 170339242, "mappedReadsCount": 115195054, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138818" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0002543", "name": "vein endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_venous_systemic, Vascular", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 25.340485, "sdRefIntergenicDistribution": 1.396188, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 44502, "distinctRankCount": 244, "maxRank": 20258.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 170339242, "mappedReadsCount": 115195054, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138818" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000624", "name": "CD4-positive, alpha-beta T cell" }, "cellTypeAuthorAnnotation": "CD4_EM/Effector, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 3.419563, "sdRefIntergenicDistribution": 2.314369, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 633808, "distinctRankCount": 882, "maxRank": 24081.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 170339242, "mappedReadsCount": 115195054, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138818" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000624", "name": "CD4-positive, alpha-beta T cell" }, "cellTypeAuthorAnnotation": "CD4_naive/CM, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 6.302712, "sdRefIntergenicDistribution": 1.750162, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 217012, "distinctRankCount": 461, "maxRank": 22518.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 170339242, "mappedReadsCount": 115195054, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138818" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0002553", "name": "fibroblast of lung" }, "cellTypeAuthorAnnotation": "Fibro_adventitial, Stroma", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 2.413394, "sdRefIntergenicDistribution": 1.705216, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 574864, "distinctRankCount": 1261, "maxRank": 24033.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 170339242, "mappedReadsCount": 115195054, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138818" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0002553", "name": "fibroblast of lung" }, "cellTypeAuthorAnnotation": "Fibro_alveolar, Stroma", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 24.959140, "sdRefIntergenicDistribution": 1.325975, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 42851, "distinctRankCount": 233, "maxRank": 20674.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 170339242, "mappedReadsCount": 115195054, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138818" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0002553", "name": "fibroblast of lung" }, "cellTypeAuthorAnnotation": "Fibro_peribronchial, Stroma", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 115.416886, "sdRefIntergenicDistribution": 1.363291, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 9385, "distinctRankCount": 89, "maxRank": 18915.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 170339242, "mappedReadsCount": 115195054, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138818" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000192", "name": "smooth muscle cell" }, "cellTypeAuthorAnnotation": "Muscle_smooth_pulmonary, Stroma", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 26.494043, "sdRefIntergenicDistribution": 1.381068, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 41100, "distinctRankCount": 227, "maxRank": 20425.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 170339242, "mappedReadsCount": 115195054, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138818" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000913", "name": "effector memory CD8-positive, alpha-beta T cell" }, "cellTypeAuthorAnnotation": "CD8_EM, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 6.737613, "sdRefIntergenicDistribution": 1.783307, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 202609, "distinctRankCount": 500, "maxRank": 22514.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 170339242, "mappedReadsCount": 115195054, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138818" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000913", "name": "effector memory CD8-positive, alpha-beta T cell" }, "cellTypeAuthorAnnotation": "CD8_EM/EMRA, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 2.944223, "sdRefIntergenicDistribution": 1.990861, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 574528, "distinctRankCount": 772, "maxRank": 23597.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 170339242, "mappedReadsCount": 115195054, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138818" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0002633", "name": "respiratory basal cell" }, "cellTypeAuthorAnnotation": "Basal, Epithelia", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 589.636416, "sdRefIntergenicDistribution": 1.029041, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1647, "distinctRankCount": 23, "maxRank": 17882.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 170339242, "mappedReadsCount": 115195054, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138818" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0001054", "name": "CD14-positive monocyte" }, "cellTypeAuthorAnnotation": "Monocyte_CD14, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 3.759535, "sdRefIntergenicDistribution": 2.051992, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 432873, "distinctRankCount": 728, "maxRank": 22892.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 170339242, "mappedReadsCount": 115195054, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138818" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000909", "name": "CD8-positive, alpha-beta memory T cell" }, "cellTypeAuthorAnnotation": "CD8_TRM, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 52.858063, "sdRefIntergenicDistribution": 1.447446, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 19172, "distinctRankCount": 112, "maxRank": 19521.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 170339242, "mappedReadsCount": 115195054, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138818" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000909", "name": "CD8-positive, alpha-beta memory T cell" }, "cellTypeAuthorAnnotation": "CD8_TRM/EM, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 8.601139, "sdRefIntergenicDistribution": 1.696859, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 149996, "distinctRankCount": 437, "maxRank": 22077.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 170339242, "mappedReadsCount": 115195054, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138818" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0002396", "name": "CD14-low, CD16-positive monocyte" }, "cellTypeAuthorAnnotation": "Monocyte_CD16, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 10.409552, "sdRefIntergenicDistribution": 1.712060, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 121709, "distinctRankCount": 401, "maxRank": 21245.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 170339242, "mappedReadsCount": 115195054, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138818" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000186", "name": "myofibroblast cell" }, "cellTypeAuthorAnnotation": "Fibro_myofibroblast, Stroma", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 107.630984, "sdRefIntergenicDistribution": 1.199814, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 9341, "distinctRankCount": 92, "maxRank": 18867.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 170339242, "mappedReadsCount": 115195054, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138818" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000623", "name": "natural killer cell" }, "cellTypeAuthorAnnotation": "NK_CD11d, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 60.025382, "sdRefIntergenicDistribution": 1.262580, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 16806, "distinctRankCount": 119, "maxRank": 19313.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 170339242, "mappedReadsCount": 115195054, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138818" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000623", "name": "natural killer cell" }, "cellTypeAuthorAnnotation": "NK_CD16hi, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 4.445601, "sdRefIntergenicDistribution": 1.913544, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 347942, "distinctRankCount": 615, "maxRank": 23227.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 170339242, "mappedReadsCount": 115195054, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138818" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000623", "name": "natural killer cell" }, "cellTypeAuthorAnnotation": "NK_CD56bright, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 13.765708, "sdRefIntergenicDistribution": 1.599421, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 86081, "distinctRankCount": 342, "maxRank": 21539.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 170339242, "mappedReadsCount": 115195054, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138818" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:1001603", "name": "lung macrophage" }, "cellTypeAuthorAnnotation": "Macro_CCL, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 46.942942, "sdRefIntergenicDistribution": 1.482735, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 23298, "distinctRankCount": 192, "maxRank": 19387.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 170339242, "mappedReadsCount": 115195054, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138818" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:1001603", "name": "lung macrophage" }, "cellTypeAuthorAnnotation": "Macro_CHIT1, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 56.875418, "sdRefIntergenicDistribution": 1.378134, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 19063, "distinctRankCount": 126, "maxRank": 19358.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 170339242, "mappedReadsCount": 115195054, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138818" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:1001603", "name": "lung macrophage" }, "cellTypeAuthorAnnotation": "Macro_intermediate, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 9.667745, "sdRefIntergenicDistribution": 1.686075, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 130813, "distinctRankCount": 475, "maxRank": 21551.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 170339242, "mappedReadsCount": 115195054, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138818" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:1001603", "name": "lung macrophage" }, "cellTypeAuthorAnnotation": "Macro_intravascular, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 20.905400, "sdRefIntergenicDistribution": 1.487178, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 54354, "distinctRankCount": 296, "maxRank": 20563.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 170339242, "mappedReadsCount": 115195054, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138818" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000897", "name": "CD4-positive, alpha-beta memory T cell" }, "cellTypeAuthorAnnotation": "CD4_TRM, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 5.256247, "sdRefIntergenicDistribution": 1.956131, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 296326, "distinctRankCount": 574, "maxRank": 23008.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 170339242, "mappedReadsCount": 115195054, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138818" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000077", "name": "mesothelial cell" }, "cellTypeAuthorAnnotation": "Mesothelia, Stroma", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 111.892446, "sdRefIntergenicDistribution": 1.240089, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 9276, "distinctRankCount": 85, "maxRank": 18654.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 170339242, "mappedReadsCount": 115195054, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138818" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000097", "name": "mast cell" }, "cellTypeAuthorAnnotation": "Mast_cell , Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 13.631118, "sdRefIntergenicDistribution": 1.853195, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 93271, "distinctRankCount": 261, "maxRank": 21456.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 170339242, "mappedReadsCount": 115195054, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138818" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:1000413", "name": "endothelial cell of artery" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_arterial_systemic, Vascular", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 1980.198020, "sdRefIntergenicDistribution": 1.000000, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 0, "distinctRankCount": 0 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 170339242, "mappedReadsCount": 115195054, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138818" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000940", "name": "mucosal invariant T cell" }, "cellTypeAuthorAnnotation": "MAIT, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 20.496453, "sdRefIntergenicDistribution": 1.465446, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 54892, "distinctRankCount": 227, "maxRank": 20543.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 170339242, "mappedReadsCount": 115195054, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138818" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0002063", "name": "type II pneumocyte" }, "cellTypeAuthorAnnotation": "AT2, Epithelia", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 9.732020, "sdRefIntergenicDistribution": 1.488436, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 120701, "distinctRankCount": 449, "maxRank": 21604.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 170339242, "mappedReadsCount": 115195054, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138818" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000987", "name": "IgA plasma cell" }, "cellTypeAuthorAnnotation": "B_plasma_IgA, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 13.537313, "sdRefIntergenicDistribution": 1.536644, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 86275, "distinctRankCount": 252, "maxRank": 20475.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 170339242, "mappedReadsCount": 115195054, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138818" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0019018", "name": "blood vessel smooth muscle cell" }, "cellTypeAuthorAnnotation": "Muscle_perivascular_immune_recruiting, Stroma", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 604.229607, "sdRefIntergenicDistribution": 1.000000, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 0, "distinctRankCount": 0 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 170339242, "mappedReadsCount": 115195054, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138818" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0019018", "name": "blood vessel smooth muscle cell" }, "cellTypeAuthorAnnotation": "Muscle_smooth_arterial_systemic, Stroma", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 2145.922747, "sdRefIntergenicDistribution": 1.000000, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 0, "distinctRankCount": 0 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 170339242, "mappedReadsCount": 115195054, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138818" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000158", "name": "club cell" }, "cellTypeAuthorAnnotation": "Secretory_Club, Epithelia", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 16.350567, "sdRefIntergenicDistribution": 1.512317, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 70321, "distinctRankCount": 225, "maxRank": 19889.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 170339242, "mappedReadsCount": 115195054, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138818" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000787", "name": "memory B cell" }, "cellTypeAuthorAnnotation": "B_memory, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 3.166725, "sdRefIntergenicDistribution": 1.987069, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 524567, "distinctRankCount": 760, "maxRank": 23348.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 170339242, "mappedReadsCount": 115195054, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138818" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0009115", "name": "lymph node lymphatic vessel endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_Lymphatic, Vascular", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 15.492364, "sdRefIntergenicDistribution": 1.424555, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 72999, "distinctRankCount": 355, "maxRank": 21249.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 170339242, "mappedReadsCount": 115195054, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138818" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000985", "name": "IgG plasma cell" }, "cellTypeAuthorAnnotation": "B_plasma_IgG, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 20.471607, "sdRefIntergenicDistribution": 1.444438, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 54433, "distinctRankCount": 169, "maxRank": 19386.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 170339242, "mappedReadsCount": 115195054, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138818" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000815", "name": "regulatory T cell" }, "cellTypeAuthorAnnotation": "T_reg, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 29.865408, "sdRefIntergenicDistribution": 1.442115, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 35928, "distinctRankCount": 164, "maxRank": 20165.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 170339242, "mappedReadsCount": 115195054, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138818" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0001065", "name": "innate lymphoid cell" }, "cellTypeAuthorAnnotation": "ILC, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 20.101951, "sdRefIntergenicDistribution": 1.495990, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 55642, "distinctRankCount": 259, "maxRank": 20887.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 170339242, "mappedReadsCount": 115195054, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138818" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000788", "name": "naive B cell" }, "cellTypeAuthorAnnotation": "B_naive, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 73.838902, "sdRefIntergenicDistribution": 1.293943, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 14076, "distinctRankCount": 120, "maxRank": 18857.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 170339242, "mappedReadsCount": 115195054, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138818" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000556", "name": "megakaryocyte" }, "cellTypeAuthorAnnotation": "Megakaryocyte, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 429.227351, "sdRefIntergenicDistribution": 1.373961, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 2104, "distinctRankCount": 28, "maxRank": 17933.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 165483782, "mappedReadsCount": 108324434, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138823" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0002144", "name": "capillary endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_Cap_a, Vascular", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 2.598042, "sdRefIntergenicDistribution": 2.374729, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 966456, "distinctRankCount": 1182, "maxRank": 24836.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 165483782, "mappedReadsCount": 108324434, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138823" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0002144", "name": "capillary endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_Cap_g, Vascular", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 6.631869, "sdRefIntergenicDistribution": 1.750113, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 205944, "distinctRankCount": 513, "maxRank": 23258.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 165483782, "mappedReadsCount": 108324434, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138823" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000583", "name": "alveolar macrophage" }, "cellTypeAuthorAnnotation": "Macro_alveolar, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 9.985853, "sdRefIntergenicDistribution": 1.483581, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 116871, "distinctRankCount": 446, "maxRank": 21536.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 165483782, "mappedReadsCount": 108324434, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138823" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0002062", "name": "type I pneumocyte" }, "cellTypeAuthorAnnotation": "AT1 , Epithelia", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 2.869197, "sdRefIntergenicDistribution": 2.169504, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 727502, "distinctRankCount": 1217, "maxRank": 24752.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 165483782, "mappedReadsCount": 108324434, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138823" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000814", "name": "mature NK T cell" }, "cellTypeAuthorAnnotation": "NKT, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 281.294766, "sdRefIntergenicDistribution": 1.218169, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 3511, "distinctRankCount": 45, "maxRank": 18221.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 165483782, "mappedReadsCount": 108324434, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138823" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:1001568", "name": "pulmonary artery endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_arterial_pulmonary, Vascular", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 19.128171, "sdRefIntergenicDistribution": 1.426347, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 57052, "distinctRankCount": 273, "maxRank": 21300.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 165483782, "mappedReadsCount": 108324434, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138823" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0009089", "name": "lung pericyte" }, "cellTypeAuthorAnnotation": "Muscle_pericyte_pulmonary, Stroma", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 19.341433, "sdRefIntergenicDistribution": 1.440936, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 56764, "distinctRankCount": 243, "maxRank": 21389.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 165483782, "mappedReadsCount": 108324434, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138823" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000798", "name": "gamma-delta T cell" }, "cellTypeAuthorAnnotation": "gdT, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 662.210093, "sdRefIntergenicDistribution": 1.286503, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1361, "distinctRankCount": 22, "maxRank": 17919.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 165483782, "mappedReadsCount": 108324434, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138823" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0002543", "name": "vein endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_venous_pulmonary, Vascular", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 48.500763, "sdRefIntergenicDistribution": 1.363441, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 21273, "distinctRankCount": 143, "maxRank": 19862.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 165483782, "mappedReadsCount": 108324434, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138823" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0002543", "name": "vein endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_venous_systemic, Vascular", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 63.455592, "sdRefIntergenicDistribution": 1.281709, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 16743, "distinctRankCount": 126, "maxRank": 19173.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 165483782, "mappedReadsCount": 108324434, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138823" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000057", "name": "fibroblast" }, "cellTypeAuthorAnnotation": "NAF_endoneurial, Stroma", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 467.758052, "sdRefIntergenicDistribution": 1.210352, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1909, "distinctRankCount": 31, "maxRank": 18015.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 165483782, "mappedReadsCount": 108324434, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138823" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0002553", "name": "fibroblast of lung" }, "cellTypeAuthorAnnotation": "Fibro_adventitial, Stroma", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 1.354395, "sdRefIntergenicDistribution": 2.591106, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 2842952, "distinctRankCount": 2836, "maxRank": 26102.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 165483782, "mappedReadsCount": 108324434, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138823" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0002553", "name": "fibroblast of lung" }, "cellTypeAuthorAnnotation": "Fibro_alveolar, Stroma", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 1.344925, "sdRefIntergenicDistribution": 2.117179, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1514611, "distinctRankCount": 1490, "maxRank": 25323.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 165483782, "mappedReadsCount": 108324434, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138823" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0002553", "name": "fibroblast of lung" }, "cellTypeAuthorAnnotation": "Fibro_immune_recruiting, Stroma", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 32.805672, "sdRefIntergenicDistribution": 1.390818, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 33988, "distinctRankCount": 271, "maxRank": 20425.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 165483782, "mappedReadsCount": 108324434, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138823" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0002553", "name": "fibroblast of lung" }, "cellTypeAuthorAnnotation": "Fibro_peribronchial, Stroma", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 50.353495, "sdRefIntergenicDistribution": 1.295291, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 21107, "distinctRankCount": 166, "maxRank": 19910.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 165483782, "mappedReadsCount": 108324434, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138823" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000192", "name": "smooth muscle cell" }, "cellTypeAuthorAnnotation": "Muscle_smooth_pulmonary, Stroma", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 11.142271, "sdRefIntergenicDistribution": 1.423109, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 101039, "distinctRankCount": 364, "maxRank": 21883.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 165483782, "mappedReadsCount": 108324434, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138823" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000913", "name": "effector memory CD8-positive, alpha-beta T cell" }, "cellTypeAuthorAnnotation": "CD8_EM/EMRA, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 225.832035, "sdRefIntergenicDistribution": 1.257981, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 4590, "distinctRankCount": 56, "maxRank": 18237.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 165483782, "mappedReadsCount": 108324434, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138823" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0002633", "name": "respiratory basal cell" }, "cellTypeAuthorAnnotation": "Basal, Epithelia", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 19.785158, "sdRefIntergenicDistribution": 1.444215, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 56407, "distinctRankCount": 319, "maxRank": 21319.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 165483782, "mappedReadsCount": 108324434, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138823" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0002633", "name": "respiratory basal cell" }, "cellTypeAuthorAnnotation": "Dividing_Basal, Epithelia", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 52.540584, "sdRefIntergenicDistribution": 1.396077, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 20740, "distinctRankCount": 177, "maxRank": 19730.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 165483782, "mappedReadsCount": 108324434, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138823" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000186", "name": "myofibroblast cell" }, "cellTypeAuthorAnnotation": "Fibro_myofibroblast, Stroma", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 6.581300, "sdRefIntergenicDistribution": 1.625118, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 194124, "distinctRankCount": 504, "maxRank": 23135.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 165483782, "mappedReadsCount": 108324434, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138823" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000623", "name": "natural killer cell" }, "cellTypeAuthorAnnotation": "NK_CD16hi, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 280.743740, "sdRefIntergenicDistribution": 1.195675, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 3330, "distinctRankCount": 35, "maxRank": 18272.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 165483782, "mappedReadsCount": 108324434, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138823" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000077", "name": "mesothelial cell" }, "cellTypeAuthorAnnotation": "Mesothelia, Stroma", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 18.970773, "sdRefIntergenicDistribution": 1.383720, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 57785, "distinctRankCount": 326, "maxRank": 21082.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 165483782, "mappedReadsCount": 108324434, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138823" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:1000413", "name": "endothelial cell of artery" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_arterial_systemic, Vascular", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 272.562427, "sdRefIntergenicDistribution": 1.181506, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 3548, "distinctRankCount": 32, "maxRank": 18327.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 165483782, "mappedReadsCount": 108324434, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138823" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0002063", "name": "type II pneumocyte" }, "cellTypeAuthorAnnotation": "AT2, Epithelia", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 4.206839, "sdRefIntergenicDistribution": 1.727022, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 322327, "distinctRankCount": 678, "maxRank": 23484.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 165483782, "mappedReadsCount": 108324434, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138823" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0019018", "name": "blood vessel smooth muscle cell" }, "cellTypeAuthorAnnotation": "Muscle_smooth_arterial_systemic, Stroma", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 366.568910, "sdRefIntergenicDistribution": 1.000000, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 0, "distinctRankCount": 0 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 165483782, "mappedReadsCount": 108324434, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138823" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000158", "name": "club cell" }, "cellTypeAuthorAnnotation": "Secretory_Club, Epithelia", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 5.242002, "sdRefIntergenicDistribution": 1.698345, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 250567, "distinctRankCount": 573, "maxRank": 23199.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 165483782, "mappedReadsCount": 108324434, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138823" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000067", "name": "ciliated epithelial cell" }, "cellTypeAuthorAnnotation": "Ciliated, Epithelia", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 2.504174, "sdRefIntergenicDistribution": 2.784151, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1723695, "distinctRankCount": 3191, "maxRank": 26228.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 165483782, "mappedReadsCount": 108324434, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138823" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0009115", "name": "lymph node lymphatic vessel endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_Lymphatic, Vascular", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 1.465158, "sdRefIntergenicDistribution": 2.620067, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 2685636, "distinctRankCount": 2290, "maxRank": 25974.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 165483782, "mappedReadsCount": 108324434, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138823" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000160", "name": "goblet cell" }, "cellTypeAuthorAnnotation": "Secretory_Goblet, Epithelia", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 16.774283, "sdRefIntergenicDistribution": 1.448337, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 67814, "distinctRankCount": 364, "maxRank": 21297.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 165483782, "mappedReadsCount": 108324434, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138823" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0002368", "name": "respiratory epithelial cell" }, "cellTypeAuthorAnnotation": "Suprabasal, Epithelia", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 97.932524, "sdRefIntergenicDistribution": 1.309800, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 10438, "distinctRankCount": 108, "maxRank": 19159.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 165483782, "mappedReadsCount": 108324434, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138823" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:4033044", "name": "deuterosomal cell" }, "cellTypeAuthorAnnotation": "Deuterosomal, Epithelia", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 57.432519, "sdRefIntergenicDistribution": 1.416875, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 18849, "distinctRankCount": 185, "maxRank": 20024.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 165483782, "mappedReadsCount": 108324434, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138823" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0001065", "name": "innate lymphoid cell" }, "cellTypeAuthorAnnotation": "ILC, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 271.088605, "sdRefIntergenicDistribution": 1.308613, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 3710, "distinctRankCount": 53, "maxRank": 18317.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 165483782, "mappedReadsCount": 108324434, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138823" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000146", "name": "simple columnar epithelial cell" }, "cellTypeAuthorAnnotation": "SMG_Duct, Epithelia", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 63.823300, "sdRefIntergenicDistribution": 1.432351, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 17025, "distinctRankCount": 138, "maxRank": 19168.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 165483782, "mappedReadsCount": 108324434, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138823" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0002376", "name": "non-myelinating Schwann cell" }, "cellTypeAuthorAnnotation": "Schwann_nonmyelinating, Stroma", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 729.677829, "sdRefIntergenicDistribution": 1.174142, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1259, "distinctRankCount": 19, "maxRank": 17869.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 166681297, "mappedReadsCount": 97342876, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138830" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0002063", "name": "type II pneumocyte" }, "cellTypeAuthorAnnotation": "AT2, Epithelia", "devStage": { "id": "HsapDv:0000123", "name": "29-year-old stage (human)" }, "devStageAuthorAnnotation": "25-30 (29 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 7.154577, "sdRefIntergenicDistribution": 1.882530, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 203878, "distinctRankCount": 765, "maxRank": 22481.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 166681297, "mappedReadsCount": 97342876, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138830" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0002063", "name": "type II pneumocyte" }, "cellTypeAuthorAnnotation": "Dividing_AT2, Epithelia", "devStage": { "id": "HsapDv:0000123", "name": "29-year-old stage (human)" }, "devStageAuthorAnnotation": "25-30 (29 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 87.225952, "sdRefIntergenicDistribution": 1.435069, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 12550, "distinctRankCount": 107, "maxRank": 18651.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 166681297, "mappedReadsCount": 97342876, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138830" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000583", "name": "alveolar macrophage" }, "cellTypeAuthorAnnotation": "Macro_alveolar, Immune", "devStage": { "id": "HsapDv:0000123", "name": "29-year-old stage (human)" }, "devStageAuthorAnnotation": "25-30 (29 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 17.534629, "sdRefIntergenicDistribution": 1.526546, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 66637, "distinctRankCount": 349, "maxRank": 20415.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 166681297, "mappedReadsCount": 97342876, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138830" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000192", "name": "smooth muscle cell" }, "cellTypeAuthorAnnotation": "Muscle_smooth_pulmonary, Stroma", "devStage": { "id": "HsapDv:0000123", "name": "29-year-old stage (human)" }, "devStageAuthorAnnotation": "25-30 (29 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 140.658812, "sdRefIntergenicDistribution": 1.358014, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 7733, "distinctRankCount": 86, "maxRank": 18365.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 166681297, "mappedReadsCount": 97342876, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138830" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:1001603", "name": "lung macrophage" }, "cellTypeAuthorAnnotation": "Macro_CHIT1, Immune", "devStage": { "id": "HsapDv:0000123", "name": "29-year-old stage (human)" }, "devStageAuthorAnnotation": "25-30 (29 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 860.851390, "sdRefIntergenicDistribution": 1.125929, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1137, "distinctRankCount": 25, "maxRank": 17812.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 166681297, "mappedReadsCount": 97342876, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138830" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:1001603", "name": "lung macrophage" }, "cellTypeAuthorAnnotation": "Macro_interstitial, Immune", "devStage": { "id": "HsapDv:0000123", "name": "29-year-old stage (human)" }, "devStageAuthorAnnotation": "25-30 (29 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 901.066650, "sdRefIntergenicDistribution": 1.389730, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1183, "distinctRankCount": 30, "maxRank": 17762.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 166681297, "mappedReadsCount": 97342876, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138830" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:1001603", "name": "lung macrophage" }, "cellTypeAuthorAnnotation": "Macro_intravascular, Immune", "devStage": { "id": "HsapDv:0000123", "name": "29-year-old stage (human)" }, "devStageAuthorAnnotation": "25-30 (29 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 41.587151, "sdRefIntergenicDistribution": 1.484386, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 27054, "distinctRankCount": 250, "maxRank": 19539.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 166681297, "mappedReadsCount": 97342876, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138830" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0002553", "name": "fibroblast of lung" }, "cellTypeAuthorAnnotation": "Fibro_adventitial, Stroma", "devStage": { "id": "HsapDv:0000123", "name": "29-year-old stage (human)" }, "devStageAuthorAnnotation": "25-30 (29 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 1300.745530, "sdRefIntergenicDistribution": 1.163003, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 762, "distinctRankCount": 18, "maxRank": 17780.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 166681297, "mappedReadsCount": 97342876, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138830" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000623", "name": "natural killer cell" }, "cellTypeAuthorAnnotation": "NK_CD11d, Immune", "devStage": { "id": "HsapDv:0000123", "name": "29-year-old stage (human)" }, "devStageAuthorAnnotation": "25-30 (29 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 901.048425, "sdRefIntergenicDistribution": 1.295087, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1055, "distinctRankCount": 19, "maxRank": 17753.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 166681297, "mappedReadsCount": 97342876, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138830" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000623", "name": "natural killer cell" }, "cellTypeAuthorAnnotation": "NK_CD16hi, Immune", "devStage": { "id": "HsapDv:0000123", "name": "29-year-old stage (human)" }, "devStageAuthorAnnotation": "25-30 (29 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 44.716151, "sdRefIntergenicDistribution": 1.403440, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 24047, "distinctRankCount": 172, "maxRank": 19491.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 166681297, "mappedReadsCount": 97342876, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138830" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000158", "name": "club cell" }, "cellTypeAuthorAnnotation": "Secretory_Club, Epithelia", "devStage": { "id": "HsapDv:0000123", "name": "29-year-old stage (human)" }, "devStageAuthorAnnotation": "25-30 (29 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 319.622292, "sdRefIntergenicDistribution": 1.341253, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 3363, "distinctRankCount": 45, "maxRank": 18012.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 166681297, "mappedReadsCount": 97342876, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138830" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000897", "name": "CD4-positive, alpha-beta memory T cell" }, "cellTypeAuthorAnnotation": "CD4_TRM, Immune", "devStage": { "id": "HsapDv:0000123", "name": "29-year-old stage (human)" }, "devStageAuthorAnnotation": "25-30 (29 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 455.475441, "sdRefIntergenicDistribution": 1.320205, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 2244, "distinctRankCount": 26, "maxRank": 17912.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 166681297, "mappedReadsCount": 97342876, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138830" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000990", "name": "conventional dendritic cell" }, "cellTypeAuthorAnnotation": "DC_1, Immune", "devStage": { "id": "HsapDv:0000123", "name": "29-year-old stage (human)" }, "devStageAuthorAnnotation": "25-30 (29 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 644.285163, "sdRefIntergenicDistribution": 1.474741, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1762, "distinctRankCount": 29, "maxRank": 17832.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 166681297, "mappedReadsCount": 97342876, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138830" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000990", "name": "conventional dendritic cell" }, "cellTypeAuthorAnnotation": "DC_2, Immune", "devStage": { "id": "HsapDv:0000123", "name": "29-year-old stage (human)" }, "devStageAuthorAnnotation": "25-30 (29 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 71.763375, "sdRefIntergenicDistribution": 1.422556, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 14966, "distinctRankCount": 152, "maxRank": 18850.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 166681297, "mappedReadsCount": 97342876, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138830" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000067", "name": "ciliated epithelial cell" }, "cellTypeAuthorAnnotation": "Ciliated, Epithelia", "devStage": { "id": "HsapDv:0000123", "name": "29-year-old stage (human)" }, "devStageAuthorAnnotation": "25-30 (29 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 953.754580, "sdRefIntergenicDistribution": 1.260156, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1052, "distinctRankCount": 20, "maxRank": 17826.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 166681297, "mappedReadsCount": 97342876, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138830" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0002144", "name": "capillary endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_Cap_a, Vascular", "devStage": { "id": "HsapDv:0000123", "name": "29-year-old stage (human)" }, "devStageAuthorAnnotation": "25-30 (29 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 1041.602588, "sdRefIntergenicDistribution": 1.273815, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 911, "distinctRankCount": 14, "maxRank": 17729.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 166681297, "mappedReadsCount": 97342876, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138830" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0009115", "name": "lymph node lymphatic vessel endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_Lymphatic, Vascular", "devStage": { "id": "HsapDv:0000123", "name": "29-year-old stage (human)" }, "devStageAuthorAnnotation": "25-30 (29 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 2132.196162, "sdRefIntergenicDistribution": 1.000000, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 0, "distinctRankCount": 0 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 166681297, "mappedReadsCount": 97342876, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138830" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0002062", "name": "type I pneumocyte" }, "cellTypeAuthorAnnotation": "AT1 , Epithelia", "devStage": { "id": "HsapDv:0000123", "name": "29-year-old stage (human)" }, "devStageAuthorAnnotation": "25-30 (29 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 9.896580, "sdRefIntergenicDistribution": 1.637793, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 125149, "distinctRankCount": 554, "maxRank": 21826.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 166681297, "mappedReadsCount": 97342876, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138830" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0001065", "name": "innate lymphoid cell" }, "cellTypeAuthorAnnotation": "ILC, Immune", "devStage": { "id": "HsapDv:0000123", "name": "29-year-old stage (human)" }, "devStageAuthorAnnotation": "25-30 (29 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 242.004982, "sdRefIntergenicDistribution": 1.405157, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 4248, "distinctRankCount": 62, "maxRank": 18106.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 166681297, "mappedReadsCount": 97342876, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138830" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0001054", "name": "CD14-positive monocyte" }, "cellTypeAuthorAnnotation": "Monocyte_CD14, Immune", "devStage": { "id": "HsapDv:0000123", "name": "29-year-old stage (human)" }, "devStageAuthorAnnotation": "25-30 (29 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 45.474783, "sdRefIntergenicDistribution": 1.461599, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 23867, "distinctRankCount": 187, "maxRank": 19434.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 166681297, "mappedReadsCount": 97342876, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138830" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000940", "name": "mucosal invariant T cell" }, "cellTypeAuthorAnnotation": "MAIT, Immune", "devStage": { "id": "HsapDv:0000123", "name": "29-year-old stage (human)" }, "devStageAuthorAnnotation": "25-30 (29 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 395.256725, "sdRefIntergenicDistribution": 1.360427, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 2638, "distinctRankCount": 30, "maxRank": 17966.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 166681297, "mappedReadsCount": 97342876, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138830" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000815", "name": "regulatory T cell" }, "cellTypeAuthorAnnotation": "T_reg, Immune", "devStage": { "id": "HsapDv:0000123", "name": "29-year-old stage (human)" }, "devStageAuthorAnnotation": "25-30 (29 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 418.525330, "sdRefIntergenicDistribution": 1.290468, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 2210, "distinctRankCount": 37, "maxRank": 17931.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 166681297, "mappedReadsCount": 97342876, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138830" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000624", "name": "CD4-positive, alpha-beta T cell" }, "cellTypeAuthorAnnotation": "CD4_EM/Effector, Immune", "devStage": { "id": "HsapDv:0000123", "name": "29-year-old stage (human)" }, "devStageAuthorAnnotation": "25-30 (29 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 35.436382, "sdRefIntergenicDistribution": 1.473170, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 31206, "distinctRankCount": 238, "maxRank": 19620.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 166681297, "mappedReadsCount": 97342876, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138830" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000624", "name": "CD4-positive, alpha-beta T cell" }, "cellTypeAuthorAnnotation": "CD4_naive/CM, Immune", "devStage": { "id": "HsapDv:0000123", "name": "29-year-old stage (human)" }, "devStageAuthorAnnotation": "25-30 (29 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 152.466561, "sdRefIntergenicDistribution": 1.356419, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 6937, "distinctRankCount": 74, "maxRank": 18377.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 166681297, "mappedReadsCount": 97342876, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138830" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000909", "name": "CD8-positive, alpha-beta memory T cell" }, "cellTypeAuthorAnnotation": "CD8_TRM/EM, Immune", "devStage": { "id": "HsapDv:0000123", "name": "29-year-old stage (human)" }, "devStageAuthorAnnotation": "25-30 (29 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 339.242908, "sdRefIntergenicDistribution": 1.391304, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 3173, "distinctRankCount": 50, "maxRank": 17943.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 166681297, "mappedReadsCount": 97342876, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138830" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000987", "name": "IgA plasma cell" }, "cellTypeAuthorAnnotation": "B_plasma_IgA, Immune", "devStage": { "id": "HsapDv:0000123", "name": "29-year-old stage (human)" }, "devStageAuthorAnnotation": "25-30 (29 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 1224.557513, "sdRefIntergenicDistribution": 1.251259, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 851, "distinctRankCount": 16, "maxRank": 17677.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 166681297, "mappedReadsCount": 97342876, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138830" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000784", "name": "plasmacytoid dendritic cell" }, "cellTypeAuthorAnnotation": "DC_plasmacytoid, Immune", "devStage": { "id": "HsapDv:0000123", "name": "29-year-old stage (human)" }, "devStageAuthorAnnotation": "25-30 (29 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 341.715533, "sdRefIntergenicDistribution": 1.311990, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 2782, "distinctRankCount": 37, "maxRank": 17979.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 166681297, "mappedReadsCount": 97342876, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138830" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000097", "name": "mast cell" }, "cellTypeAuthorAnnotation": "Mast_cell , Immune", "devStage": { "id": "HsapDv:0000123", "name": "29-year-old stage (human)" }, "devStageAuthorAnnotation": "25-30 (29 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 87.823655, "sdRefIntergenicDistribution": 1.375902, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 12222, "distinctRankCount": 113, "maxRank": 18696.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 166681297, "mappedReadsCount": 97342876, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138830" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000319", "name": "mucus secreting cell" }, "cellTypeAuthorAnnotation": "SMG_Mucous, Epithelia", "devStage": { "id": "HsapDv:0000123", "name": "29-year-old stage (human)" }, "devStageAuthorAnnotation": "25-30 (29 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 1175.900625, "sdRefIntergenicDistribution": 1.133933, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 817, "distinctRankCount": 23, "maxRank": 17764.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 166681297, "mappedReadsCount": 97342876, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138830" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0002633", "name": "respiratory basal cell" }, "cellTypeAuthorAnnotation": "Dividing_Basal, Epithelia", "devStage": { "id": "HsapDv:0000123", "name": "29-year-old stage (human)" }, "devStageAuthorAnnotation": "25-30 (29 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 1435.906620, "sdRefIntergenicDistribution": 1.251444, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 639, "distinctRankCount": 18, "maxRank": 17665.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 166681297, "mappedReadsCount": 97342876, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138830" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0002396", "name": "CD14-low, CD16-positive monocyte" }, "cellTypeAuthorAnnotation": "Monocyte_CD16, Immune", "devStage": { "id": "HsapDv:0000123", "name": "29-year-old stage (human)" }, "devStageAuthorAnnotation": "25-30 (29 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 16.230819, "sdRefIntergenicDistribution": 1.571021, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 72528, "distinctRankCount": 418, "maxRank": 20627.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 166681297, "mappedReadsCount": 97342876, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138830" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000814", "name": "mature NK T cell" }, "cellTypeAuthorAnnotation": "NKT, Immune", "devStage": { "id": "HsapDv:0000123", "name": "29-year-old stage (human)" }, "devStageAuthorAnnotation": "25-30 (29 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 194.920634, "sdRefIntergenicDistribution": 1.375815, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 5558, "distinctRankCount": 62, "maxRank": 18245.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 166681297, "mappedReadsCount": 97342876, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138830" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000787", "name": "memory B cell" }, "cellTypeAuthorAnnotation": "B_memory, Immune", "devStage": { "id": "HsapDv:0000123", "name": "29-year-old stage (human)" }, "devStageAuthorAnnotation": "25-30 (29 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 378.548308, "sdRefIntergenicDistribution": 1.342745, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 2768, "distinctRankCount": 48, "maxRank": 17879.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 166681297, "mappedReadsCount": 97342876, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138830" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000798", "name": "gamma-delta T cell" }, "cellTypeAuthorAnnotation": "gdT, Immune", "devStage": { "id": "HsapDv:0000123", "name": "29-year-old stage (human)" }, "devStageAuthorAnnotation": "25-30 (29 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 747.938064, "sdRefIntergenicDistribution": 1.482990, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1374, "distinctRankCount": 22, "maxRank": 17795.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 166681297, "mappedReadsCount": 97342876, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138830" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000913", "name": "effector memory CD8-positive, alpha-beta T cell" }, "cellTypeAuthorAnnotation": "CD8_EM, Immune", "devStage": { "id": "HsapDv:0000123", "name": "29-year-old stage (human)" }, "devStageAuthorAnnotation": "25-30 (29 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 61.863814, "sdRefIntergenicDistribution": 1.368818, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 16921, "distinctRankCount": 127, "maxRank": 19031.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 166681297, "mappedReadsCount": 97342876, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138830" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000913", "name": "effector memory CD8-positive, alpha-beta T cell" }, "cellTypeAuthorAnnotation": "CD8_EM/EMRA, Immune", "devStage": { "id": "HsapDv:0000123", "name": "29-year-old stage (human)" }, "devStageAuthorAnnotation": "25-30 (29 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 39.560405, "sdRefIntergenicDistribution": 1.406166, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 27210, "distinctRankCount": 184, "maxRank": 19490.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 985064374, "mappedReadsCount": 583447604, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138838" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002144", "name": "capillary endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_Cap_a, Vascular", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 21.374313, "sdRefIntergenicDistribution": 1.405425, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 49727, "distinctRankCount": 1674, "maxRank": 21661.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 985064374, "mappedReadsCount": 583447604, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138838" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002144", "name": "capillary endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_Cap_g, Vascular", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 12.970293, "sdRefIntergenicDistribution": 1.491876, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 86341, "distinctRankCount": 2120, "maxRank": 22592.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 985064374, "mappedReadsCount": 583447604, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138838" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000067", "name": "ciliated epithelial cell" }, "cellTypeAuthorAnnotation": "Ciliated, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 6.092955, "sdRefIntergenicDistribution": 1.987036, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 229129, "distinctRankCount": 3400, "maxRank": 24226.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 985064374, "mappedReadsCount": 583447604, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138838" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002396", "name": "CD14-low, CD16-positive monocyte" }, "cellTypeAuthorAnnotation": "Monocyte_CD16, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 18.014855, "sdRefIntergenicDistribution": 1.427658, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 58592, "distinctRankCount": 1758, "maxRank": 21787.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 985064374, "mappedReadsCount": 583447604, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138838" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000909", "name": "CD8-positive, alpha-beta memory T cell" }, "cellTypeAuthorAnnotation": "CD8_TRM, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 23.140368, "sdRefIntergenicDistribution": 1.369953, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 44688, "distinctRankCount": 1510, "maxRank": 21567.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 985064374, "mappedReadsCount": 583447604, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138838" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000909", "name": "CD8-positive, alpha-beta memory T cell" }, "cellTypeAuthorAnnotation": "CD8_TRM/EM, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 14.507669, "sdRefIntergenicDistribution": 1.493915, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 77654, "distinctRankCount": 1869, "maxRank": 22068.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 985064374, "mappedReadsCount": 583447604, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138838" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000897", "name": "CD4-positive, alpha-beta memory T cell" }, "cellTypeAuthorAnnotation": "CD4_TRM, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 29.132957, "sdRefIntergenicDistribution": 1.696077, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 40076, "distinctRankCount": 1456, "maxRank": 21130.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 985064374, "mappedReadsCount": 583447604, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138838" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000146", "name": "simple columnar epithelial cell" }, "cellTypeAuthorAnnotation": "SMG_Duct, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 8.674573, "sdRefIntergenicDistribution": 1.533437, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 134282, "distinctRankCount": 2647, "maxRank": 22809.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 985064374, "mappedReadsCount": 583447604, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138838" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000097", "name": "mast cell" }, "cellTypeAuthorAnnotation": "Mast_cell , Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 31.687049, "sdRefIntergenicDistribution": 1.414576, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 32418, "distinctRankCount": 1376, "maxRank": 20812.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 985064374, "mappedReadsCount": 583447604, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138838" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002633", "name": "respiratory basal cell" }, "cellTypeAuthorAnnotation": "Basal, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 15.581504, "sdRefIntergenicDistribution": 1.492093, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 71193, "distinctRankCount": 2088, "maxRank": 21843.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 985064374, "mappedReadsCount": 583447604, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138838" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000624", "name": "CD4-positive, alpha-beta T cell" }, "cellTypeAuthorAnnotation": "CD4_EM/Effector, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 6.740505, "sdRefIntergenicDistribution": 1.594381, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 176953, "distinctRankCount": 2720, "maxRank": 23890.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 985064374, "mappedReadsCount": 583447604, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138838" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000624", "name": "CD4-positive, alpha-beta T cell" }, "cellTypeAuthorAnnotation": "CD4_naive/CM, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 15.508831, "sdRefIntergenicDistribution": 1.458130, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 70253, "distinctRankCount": 1779, "maxRank": 22156.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 985064374, "mappedReadsCount": 583447604, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138838" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000583", "name": "alveolar macrophage" }, "cellTypeAuthorAnnotation": "Macro_alveolar, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 11.582811, "sdRefIntergenicDistribution": 1.624403, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 98916, "distinctRankCount": 2484, "maxRank": 22596.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 985064374, "mappedReadsCount": 583447604, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138838" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000583", "name": "alveolar macrophage" }, "cellTypeAuthorAnnotation": "Macro_alveolar_metallothioneins, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 757.790211, "sdRefIntergenicDistribution": 1.183796, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1272, "distinctRankCount": 89, "maxRank": 17971.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 985064374, "mappedReadsCount": 583447604, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138838" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000815", "name": "regulatory T cell" }, "cellTypeAuthorAnnotation": "T_reg, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 30.927845, "sdRefIntergenicDistribution": 1.351899, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 33454, "distinctRankCount": 1289, "maxRank": 21032.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 985064374, "mappedReadsCount": 583447604, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138838" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002553", "name": "fibroblast of lung" }, "cellTypeAuthorAnnotation": "Fibro_adventitial, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 3.838234, "sdRefIntergenicDistribution": 1.833076, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 370896, "distinctRankCount": 3625, "maxRank": 25216.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 985064374, "mappedReadsCount": 583447604, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138838" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002553", "name": "fibroblast of lung" }, "cellTypeAuthorAnnotation": "Fibro_alveolar, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 2.520249, "sdRefIntergenicDistribution": 2.062332, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 675153, "distinctRankCount": 4238, "maxRank": 25955.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 985064374, "mappedReadsCount": 583447604, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138838" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002553", "name": "fibroblast of lung" }, "cellTypeAuthorAnnotation": "Fibro_peribronchial, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 42.383512, "sdRefIntergenicDistribution": 1.358633, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 24104, "distinctRankCount": 1191, "maxRank": 20458.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 985064374, "mappedReadsCount": 583447604, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138838" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002553", "name": "fibroblast of lung" }, "cellTypeAuthorAnnotation": "Fibro_perichondrial, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 170.939045, "sdRefIntergenicDistribution": 1.260107, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 5864, "distinctRankCount": 414, "maxRank": 18598.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 985064374, "mappedReadsCount": 583447604, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138838" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002553", "name": "fibroblast of lung" }, "cellTypeAuthorAnnotation": "Fibro_perichondrial, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 37.814196, "sdRefIntergenicDistribution": 1.414549, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 28106, "distinctRankCount": 1291, "maxRank": 20285.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 985064374, "mappedReadsCount": 583447604, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138838" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:1001603", "name": "lung macrophage" }, "cellTypeAuthorAnnotation": "Macro_CCL, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 265.290513, "sdRefIntergenicDistribution": 1.157671, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 3335, "distinctRankCount": 187, "maxRank": 18312.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 985064374, "mappedReadsCount": 583447604, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138838" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:1001603", "name": "lung macrophage" }, "cellTypeAuthorAnnotation": "Macro_CHIT1, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 120.216174, "sdRefIntergenicDistribution": 1.440818, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 8745, "distinctRankCount": 419, "maxRank": 18905.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 985064374, "mappedReadsCount": 583447604, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138838" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:1001603", "name": "lung macrophage" }, "cellTypeAuthorAnnotation": "Macro_intermediate, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 31.785981, "sdRefIntergenicDistribution": 1.351439, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 33154, "distinctRankCount": 1336, "maxRank": 20757.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 985064374, "mappedReadsCount": 583447604, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138838" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:1001603", "name": "lung macrophage" }, "cellTypeAuthorAnnotation": "Macro_interstitial, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 989.158897, "sdRefIntergenicDistribution": 1.013700, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 935, "distinctRankCount": 29, "maxRank": 17851.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 985064374, "mappedReadsCount": 583447604, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138838" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:1001603", "name": "lung macrophage" }, "cellTypeAuthorAnnotation": "Macro_intravascular, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 12.784275, "sdRefIntergenicDistribution": 1.511350, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 87150, "distinctRankCount": 2145, "maxRank": 22442.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 985064374, "mappedReadsCount": 583447604, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138838" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000623", "name": "natural killer cell" }, "cellTypeAuthorAnnotation": "NK_CD11d, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 94.459702, "sdRefIntergenicDistribution": 1.275424, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 10426, "distinctRankCount": 577, "maxRank": 19387.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 985064374, "mappedReadsCount": 583447604, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138838" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000623", "name": "natural killer cell" }, "cellTypeAuthorAnnotation": "NK_CD16hi, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 7.514566, "sdRefIntergenicDistribution": 1.614384, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 158030, "distinctRankCount": 2534, "maxRank": 23879.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 985064374, "mappedReadsCount": 583447604, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138838" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000623", "name": "natural killer cell" }, "cellTypeAuthorAnnotation": "NK_CD56bright, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 97.047847, "sdRefIntergenicDistribution": 1.320286, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 10596, "distinctRankCount": 567, "maxRank": 19311.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 985064374, "mappedReadsCount": 583447604, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138838" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000985", "name": "IgG plasma cell" }, "cellTypeAuthorAnnotation": "B_plasma_IgG, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 96.954712, "sdRefIntergenicDistribution": 1.363448, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 10758, "distinctRankCount": 576, "maxRank": 19183.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 985064374, "mappedReadsCount": 583447604, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138838" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0009115", "name": "lymph node lymphatic vessel endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_Lymphatic, Vascular", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 7.831034, "sdRefIntergenicDistribution": 1.592493, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 148809, "distinctRankCount": 2872, "maxRank": 23798.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 985064374, "mappedReadsCount": 583447604, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138838" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000913", "name": "effector memory CD8-positive, alpha-beta T cell" }, "cellTypeAuthorAnnotation": "CD8_EM, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 18.836832, "sdRefIntergenicDistribution": 1.406437, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 56972, "distinctRankCount": 1561, "maxRank": 21466.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 985064374, "mappedReadsCount": 583447604, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138838" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000913", "name": "effector memory CD8-positive, alpha-beta T cell" }, "cellTypeAuthorAnnotation": "CD8_EM/EMRA, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 50.206943, "sdRefIntergenicDistribution": 1.384301, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 20330, "distinctRankCount": 961, "maxRank": 20278.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 985064374, "mappedReadsCount": 583447604, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138838" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000186", "name": "myofibroblast cell" }, "cellTypeAuthorAnnotation": "Fibro_myofibroblast, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 86.102411, "sdRefIntergenicDistribution": 1.291340, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 11771, "distinctRankCount": 694, "maxRank": 19458.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 985064374, "mappedReadsCount": 583447604, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138838" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000158", "name": "club cell" }, "cellTypeAuthorAnnotation": "Secretory_Club, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 4.460642, "sdRefIntergenicDistribution": 1.789642, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 302155, "distinctRankCount": 3343, "maxRank": 24841.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 985064374, "mappedReadsCount": 583447604, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138838" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0001065", "name": "innate lymphoid cell" }, "cellTypeAuthorAnnotation": "ILC, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 257.771438, "sdRefIntergenicDistribution": 1.237746, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 3821, "distinctRankCount": 254, "maxRank": 18471.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 985064374, "mappedReadsCount": 583447604, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138838" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000192", "name": "smooth muscle cell" }, "cellTypeAuthorAnnotation": "Muscle_smooth_pulmonary, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 11.286035, "sdRefIntergenicDistribution": 1.479521, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 98047, "distinctRankCount": 2364, "maxRank": 22694.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 985064374, "mappedReadsCount": 583447604, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138838" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0019001", "name": "tracheobronchial serous cell" }, "cellTypeAuthorAnnotation": "SMG_Serous, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 1.151367, "sdRefIntergenicDistribution": 2.434499, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 2296601, "distinctRankCount": 5923, "maxRank": 26802.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 985064374, "mappedReadsCount": 583447604, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138838" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0019019", "name": "tracheobronchial smooth muscle cell" }, "cellTypeAuthorAnnotation": "Muscle_smooth_airway, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 722.049596, "sdRefIntergenicDistribution": 1.239425, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1307, "distinctRankCount": 59, "maxRank": 17933.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 985064374, "mappedReadsCount": 583447604, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138838" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000990", "name": "conventional dendritic cell" }, "cellTypeAuthorAnnotation": "DC_1, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 154.768559, "sdRefIntergenicDistribution": 1.358743, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 6244, "distinctRankCount": 405, "maxRank": 18763.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 985064374, "mappedReadsCount": 583447604, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138838" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000990", "name": "conventional dendritic cell" }, "cellTypeAuthorAnnotation": "DC_2, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 49.058502, "sdRefIntergenicDistribution": 1.352613, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 20929, "distinctRankCount": 1301, "maxRank": 20120.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 985064374, "mappedReadsCount": 583447604, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138838" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000990", "name": "conventional dendritic cell" }, "cellTypeAuthorAnnotation": "DC_activated, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 668.464045, "sdRefIntergenicDistribution": 1.226844, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1479, "distinctRankCount": 81, "maxRank": 17884.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 985064374, "mappedReadsCount": 583447604, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138838" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0019018", "name": "blood vessel smooth muscle cell" }, "cellTypeAuthorAnnotation": "Muscle_perivascular_immune_recruiting, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 57.742452, "sdRefIntergenicDistribution": 1.318133, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 17870, "distinctRankCount": 948, "maxRank": 19683.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 985064374, "mappedReadsCount": 583447604, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138838" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0001054", "name": "CD14-positive monocyte" }, "cellTypeAuthorAnnotation": "Monocyte_CD14, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 25.166618, "sdRefIntergenicDistribution": 1.341949, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 40754, "distinctRankCount": 1474, "maxRank": 21304.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 985064374, "mappedReadsCount": 583447604, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138838" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002063", "name": "type II pneumocyte" }, "cellTypeAuthorAnnotation": "AT2, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 1.102186, "sdRefIntergenicDistribution": 2.698686, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 3035877, "distinctRankCount": 6300, "maxRank": 27336.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 985064374, "mappedReadsCount": 583447604, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138838" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002063", "name": "type II pneumocyte" }, "cellTypeAuthorAnnotation": "Dividing_AT2, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 17.954006, "sdRefIntergenicDistribution": 1.470236, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 60896, "distinctRankCount": 2364, "maxRank": 21833.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 985064374, "mappedReadsCount": 583447604, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138838" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002543", "name": "vein endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_venous_pulmonary, Vascular", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 21.130071, "sdRefIntergenicDistribution": 1.398752, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 49646, "distinctRankCount": 1660, "maxRank": 21658.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 985064374, "mappedReadsCount": 583447604, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138838" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002543", "name": "vein endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_venous_systemic, Vascular", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 20.676807, "sdRefIntergenicDistribution": 1.389695, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 50957, "distinctRankCount": 1936, "maxRank": 21562.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 985064374, "mappedReadsCount": 583447604, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138838" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0009089", "name": "lung pericyte" }, "cellTypeAuthorAnnotation": "Muscle_pericyte_pulmonary, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 63.311585, "sdRefIntergenicDistribution": 1.251263, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 15748, "distinctRankCount": 878, "maxRank": 19900.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 985064374, "mappedReadsCount": 583447604, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138838" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000814", "name": "mature NK T cell" }, "cellTypeAuthorAnnotation": "NKT, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 28.516896, "sdRefIntergenicDistribution": 1.349648, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 36280, "distinctRankCount": 1336, "maxRank": 21259.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 985064374, "mappedReadsCount": 583447604, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138838" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000160", "name": "goblet cell" }, "cellTypeAuthorAnnotation": "Secretory_Goblet, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 12.445388, "sdRefIntergenicDistribution": 1.524776, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 92737, "distinctRankCount": 2509, "maxRank": 22238.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 985064374, "mappedReadsCount": 583447604, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138838" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000940", "name": "mucosal invariant T cell" }, "cellTypeAuthorAnnotation": "MAIT, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 46.549677, "sdRefIntergenicDistribution": 1.346895, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 22008, "distinctRankCount": 993, "maxRank": 20169.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 985064374, "mappedReadsCount": 583447604, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138838" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000319", "name": "mucus secreting cell" }, "cellTypeAuthorAnnotation": "SMG_Mucous, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 1.214974, "sdRefIntergenicDistribution": 2.350781, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1975602, "distinctRankCount": 5827, "maxRank": 26667.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 985064374, "mappedReadsCount": 583447604, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138838" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:1001568", "name": "pulmonary artery endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_arterial_pulmonary, Vascular", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 53.997402, "sdRefIntergenicDistribution": 1.349190, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 19074, "distinctRankCount": 934, "maxRank": 20163.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 985064374, "mappedReadsCount": 583447604, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138838" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000185", "name": "myoepithelial cell" }, "cellTypeAuthorAnnotation": "Myoepithelial, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 4.243305, "sdRefIntergenicDistribution": 1.739196, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 315142, "distinctRankCount": 3465, "maxRank": 24301.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 985064374, "mappedReadsCount": 583447604, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138838" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000798", "name": "gamma-delta T cell" }, "cellTypeAuthorAnnotation": "gdT, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 147.292675, "sdRefIntergenicDistribution": 1.259153, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 6799, "distinctRankCount": 393, "maxRank": 18889.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 985064374, "mappedReadsCount": 583447604, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138838" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000788", "name": "naive B cell" }, "cellTypeAuthorAnnotation": "B_naive, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 116.307192, "sdRefIntergenicDistribution": 1.238193, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 8267, "distinctRankCount": 473, "maxRank": 19101.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 985064374, "mappedReadsCount": 583447604, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138838" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000235", "name": "macrophage" }, "cellTypeAuthorAnnotation": "Macro_AW_CX3CR1, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 66.484733, "sdRefIntergenicDistribution": 1.303814, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 15200, "distinctRankCount": 837, "maxRank": 19751.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 985064374, "mappedReadsCount": 583447604, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138838" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000987", "name": "IgA plasma cell" }, "cellTypeAuthorAnnotation": "B_plasma_IgA, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 7.407650, "sdRefIntergenicDistribution": 1.725394, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 168972, "distinctRankCount": 2528, "maxRank": 23028.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 985064374, "mappedReadsCount": 583447604, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138838" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000057", "name": "fibroblast" }, "cellTypeAuthorAnnotation": "NAF_perineurial, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 407.675445, "sdRefIntergenicDistribution": 1.254857, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 2351, "distinctRankCount": 176, "maxRank": 18092.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 985064374, "mappedReadsCount": 583447604, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138838" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002376", "name": "non-myelinating Schwann cell" }, "cellTypeAuthorAnnotation": "Schwann_nonmyelinating, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 47.822330, "sdRefIntergenicDistribution": 1.286304, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 21246, "distinctRankCount": 1147, "maxRank": 19923.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 985064374, "mappedReadsCount": 583447604, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138838" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000787", "name": "memory B cell" }, "cellTypeAuthorAnnotation": "B_memory, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 82.527778, "sdRefIntergenicDistribution": 1.285826, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 12081, "distinctRankCount": 582, "maxRank": 19380.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 985064374, "mappedReadsCount": 583447604, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138838" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000138", "name": "chondrocyte" }, "cellTypeAuthorAnnotation": "Chondrocyte, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 2.660665, "sdRefIntergenicDistribution": 2.068874, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 639316, "distinctRankCount": 4249, "maxRank": 25500.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 985064374, "mappedReadsCount": 583447604, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138838" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002368", "name": "respiratory epithelial cell" }, "cellTypeAuthorAnnotation": "Suprabasal, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 102.193890, "sdRefIntergenicDistribution": 1.280756, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 9970, "distinctRankCount": 556, "maxRank": 19060.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 985064374, "mappedReadsCount": 583447604, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138838" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000165", "name": "neuroendocrine cell" }, "cellTypeAuthorAnnotation": "Neuroendocrine, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 355.184196, "sdRefIntergenicDistribution": 1.214864, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 2679, "distinctRankCount": 155, "maxRank": 18236.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 985064374, "mappedReadsCount": 583447604, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138838" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:1000413", "name": "endothelial cell of artery" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_arterial_systemic, Vascular", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 373.425444, "sdRefIntergenicDistribution": 1.235530, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 2714, "distinctRankCount": 159, "maxRank": 18066.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 985064374, "mappedReadsCount": 583447604, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138838" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000784", "name": "plasmacytoid dendritic cell" }, "cellTypeAuthorAnnotation": "DC_plasmacytoid, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 775.487784, "sdRefIntergenicDistribution": 1.193086, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1284, "distinctRankCount": 85, "maxRank": 17882.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 985064374, "mappedReadsCount": 583447604, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138838" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002062", "name": "type I pneumocyte" }, "cellTypeAuthorAnnotation": "AT1 , Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 1.833165, "sdRefIntergenicDistribution": 2.313421, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1121786, "distinctRankCount": 4912, "maxRank": 26334.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 195701754, "mappedReadsCount": 69387215, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138841" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008952", "name": "upper lobe of left lung" }, "anatEntityAuthorAnnotation": "Upper left lobe", "cellType": { "id": "CL:0002062", "name": "type I pneumocyte" }, "cellTypeAuthorAnnotation": "AT1 , Epithelia", "devStage": { "id": "HsapDv:0000158", "name": "64-year-old stage (human)" }, "devStageAuthorAnnotation": "60-64 (64 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 46.123769, "sdRefIntergenicDistribution": 2.044730, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 23884, "distinctRankCount": 1212, "maxRank": 19814.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 195701754, "mappedReadsCount": 69387215, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138841" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008952", "name": "upper lobe of left lung" }, "anatEntityAuthorAnnotation": "Upper left lobe", "cellType": { "id": "CL:0000067", "name": "ciliated epithelial cell" }, "cellTypeAuthorAnnotation": "Ciliated, Epithelia", "devStage": { "id": "HsapDv:0000158", "name": "64-year-old stage (human)" }, "devStageAuthorAnnotation": "60-64 (64 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 405.209508, "sdRefIntergenicDistribution": 1.822454, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 2478, "distinctRankCount": 204, "maxRank": 18055.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 195701754, "mappedReadsCount": 69387215, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138841" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008952", "name": "upper lobe of left lung" }, "anatEntityAuthorAnnotation": "Upper left lobe", "cellType": { "id": "CL:0002396", "name": "CD14-low, CD16-positive monocyte" }, "cellTypeAuthorAnnotation": "Monocyte_CD16, Immune", "devStage": { "id": "HsapDv:0000158", "name": "64-year-old stage (human)" }, "devStageAuthorAnnotation": "60-64 (64 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 4940.702203, "sdRefIntergenicDistribution": 1.184986, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 184, "distinctRankCount": 14, "maxRank": 17633.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 195701754, "mappedReadsCount": 69387215, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138841" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008952", "name": "upper lobe of left lung" }, "anatEntityAuthorAnnotation": "Upper left lobe", "cellType": { "id": "CL:0002144", "name": "capillary endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_Cap_g, Vascular", "devStage": { "id": "HsapDv:0000158", "name": "64-year-old stage (human)" }, "devStageAuthorAnnotation": "60-64 (64 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 1908.268912, "sdRefIntergenicDistribution": 1.593514, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 524, "distinctRankCount": 57, "maxRank": 17705.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 195701754, "mappedReadsCount": 69387215, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138841" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008952", "name": "upper lobe of left lung" }, "anatEntityAuthorAnnotation": "Upper left lobe", "cellType": { "id": "CL:0002553", "name": "fibroblast of lung" }, "cellTypeAuthorAnnotation": "Fibro_adventitial, Stroma", "devStage": { "id": "HsapDv:0000158", "name": "64-year-old stage (human)" }, "devStageAuthorAnnotation": "60-64 (64 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 1280.156164, "sdRefIntergenicDistribution": 1.537168, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 736, "distinctRankCount": 75, "maxRank": 17764.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 195701754, "mappedReadsCount": 69387215, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138841" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008952", "name": "upper lobe of left lung" }, "anatEntityAuthorAnnotation": "Upper left lobe", "cellType": { "id": "CL:0002553", "name": "fibroblast of lung" }, "cellTypeAuthorAnnotation": "Fibro_alveolar, Stroma", "devStage": { "id": "HsapDv:0000158", "name": "64-year-old stage (human)" }, "devStageAuthorAnnotation": "60-64 (64 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 626.997645, "sdRefIntergenicDistribution": 1.506368, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1438, "distinctRankCount": 139, "maxRank": 17919.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 195701754, "mappedReadsCount": 69387215, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138841" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008952", "name": "upper lobe of left lung" }, "anatEntityAuthorAnnotation": "Upper left lobe", "cellType": { "id": "CL:0002543", "name": "vein endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_venous_systemic, Vascular", "devStage": { "id": "HsapDv:0000158", "name": "64-year-old stage (human)" }, "devStageAuthorAnnotation": "60-64 (64 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 1448.195531, "sdRefIntergenicDistribution": 1.526097, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 647, "distinctRankCount": 53, "maxRank": 17743.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 195701754, "mappedReadsCount": 69387215, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138841" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008952", "name": "upper lobe of left lung" }, "anatEntityAuthorAnnotation": "Upper left lobe", "cellType": { "id": "CL:0000160", "name": "goblet cell" }, "cellTypeAuthorAnnotation": "Secretory_Goblet, Epithelia", "devStage": { "id": "HsapDv:0000158", "name": "64-year-old stage (human)" }, "devStageAuthorAnnotation": "60-64 (64 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 1921.777247, "sdRefIntergenicDistribution": 1.592012, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 509, "distinctRankCount": 48, "maxRank": 17708.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 195701754, "mappedReadsCount": 69387215, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138841" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008952", "name": "upper lobe of left lung" }, "anatEntityAuthorAnnotation": "Upper left lobe", "cellType": { "id": "CL:0002063", "name": "type II pneumocyte" }, "cellTypeAuthorAnnotation": "AT2, Epithelia", "devStage": { "id": "HsapDv:0000158", "name": "64-year-old stage (human)" }, "devStageAuthorAnnotation": "60-64 (64 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 29.910962, "sdRefIntergenicDistribution": 1.945401, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 36154, "distinctRankCount": 1458, "maxRank": 20424.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 195701754, "mappedReadsCount": 69387215, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138841" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008952", "name": "upper lobe of left lung" }, "anatEntityAuthorAnnotation": "Upper left lobe", "cellType": { "id": "CL:0002063", "name": "type II pneumocyte" }, "cellTypeAuthorAnnotation": "Dividing_AT2, Epithelia", "devStage": { "id": "HsapDv:0000158", "name": "64-year-old stage (human)" }, "devStageAuthorAnnotation": "60-64 (64 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 681.629436, "sdRefIntergenicDistribution": 1.873034, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1535, "distinctRankCount": 154, "maxRank": 17881.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 195701754, "mappedReadsCount": 69387215, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138841" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008952", "name": "upper lobe of left lung" }, "anatEntityAuthorAnnotation": "Upper left lobe", "cellType": { "id": "CL:0000583", "name": "alveolar macrophage" }, "cellTypeAuthorAnnotation": "Macro_alveolar, Immune", "devStage": { "id": "HsapDv:0000158", "name": "64-year-old stage (human)" }, "devStageAuthorAnnotation": "60-64 (64 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 26.446993, "sdRefIntergenicDistribution": 2.174889, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 41963, "distinctRankCount": 1411, "maxRank": 20634.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 195701754, "mappedReadsCount": 69387215, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138841" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008952", "name": "upper lobe of left lung" }, "anatEntityAuthorAnnotation": "Upper left lobe", "cellType": { "id": "CL:0000319", "name": "mucus secreting cell" }, "cellTypeAuthorAnnotation": "SMG_Mucous, Epithelia", "devStage": { "id": "HsapDv:0000158", "name": "64-year-old stage (human)" }, "devStageAuthorAnnotation": "60-64 (64 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 293.796622, "sdRefIntergenicDistribution": 1.707160, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 3259, "distinctRankCount": 293, "maxRank": 18200.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 195701754, "mappedReadsCount": 69387215, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138841" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008952", "name": "upper lobe of left lung" }, "anatEntityAuthorAnnotation": "Upper left lobe", "cellType": { "id": "CL:0009115", "name": "lymph node lymphatic vessel endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_Lymphatic, Vascular", "devStage": { "id": "HsapDv:0000158", "name": "64-year-old stage (human)" }, "devStageAuthorAnnotation": "60-64 (64 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 144.360405, "sdRefIntergenicDistribution": 1.821046, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 6767, "distinctRankCount": 517, "maxRank": 18592.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 195701754, "mappedReadsCount": 69387215, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138841" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008952", "name": "upper lobe of left lung" }, "anatEntityAuthorAnnotation": "Upper left lobe", "cellType": { "id": "CL:0000158", "name": "club cell" }, "cellTypeAuthorAnnotation": "Secretory_Club, Epithelia", "devStage": { "id": "HsapDv:0000158", "name": "64-year-old stage (human)" }, "devStageAuthorAnnotation": "60-64 (64 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 573.793489, "sdRefIntergenicDistribution": 1.666445, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1746, "distinctRankCount": 167, "maxRank": 18013.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 195701754, "mappedReadsCount": 69387215, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138841" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008952", "name": "upper lobe of left lung" }, "anatEntityAuthorAnnotation": "Upper left lobe", "cellType": { "id": "CL:0000077", "name": "mesothelial cell" }, "cellTypeAuthorAnnotation": "Mesothelia, Stroma", "devStage": { "id": "HsapDv:0000158", "name": "64-year-old stage (human)" }, "devStageAuthorAnnotation": "60-64 (64 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 935.885644, "sdRefIntergenicDistribution": 1.765021, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1129, "distinctRankCount": 118, "maxRank": 17839.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 195701754, "mappedReadsCount": 69387215, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138841" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008952", "name": "upper lobe of left lung" }, "anatEntityAuthorAnnotation": "Upper left lobe", "cellType": { "id": "CL:0002633", "name": "respiratory basal cell" }, "cellTypeAuthorAnnotation": "Basal, Epithelia", "devStage": { "id": "HsapDv:0000158", "name": "64-year-old stage (human)" }, "devStageAuthorAnnotation": "60-64 (64 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 1312.468466, "sdRefIntergenicDistribution": 1.708585, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 738, "distinctRankCount": 74, "maxRank": 17766.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 177386680, "mappedReadsCount": 99551829, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138845" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008952", "name": "upper lobe of left lung" }, "anatEntityAuthorAnnotation": "Upper left lobe", "cellType": { "id": "CL:0002062", "name": "type I pneumocyte" }, "cellTypeAuthorAnnotation": "AT1 , Epithelia", "devStage": { "id": "HsapDv:0000158", "name": "64-year-old stage (human)" }, "devStageAuthorAnnotation": "60-64 (64 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 0.915772, "sdRefIntergenicDistribution": 2.790716, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 3639288, "distinctRankCount": 6023, "maxRank": 27478.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 177386680, "mappedReadsCount": 99551829, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138845" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008952", "name": "upper lobe of left lung" }, "anatEntityAuthorAnnotation": "Upper left lobe", "cellType": { "id": "CL:0000067", "name": "ciliated epithelial cell" }, "cellTypeAuthorAnnotation": "Ciliated, Epithelia", "devStage": { "id": "HsapDv:0000158", "name": "64-year-old stage (human)" }, "devStageAuthorAnnotation": "60-64 (64 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 9.434902, "sdRefIntergenicDistribution": 1.953655, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 137996, "distinctRankCount": 2851, "maxRank": 23012.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 177386680, "mappedReadsCount": 99551829, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138845" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008952", "name": "upper lobe of left lung" }, "anatEntityAuthorAnnotation": "Upper left lobe", "cellType": { "id": "CL:0002396", "name": "CD14-low, CD16-positive monocyte" }, "cellTypeAuthorAnnotation": "Monocyte_CD16, Immune", "devStage": { "id": "HsapDv:0000158", "name": "64-year-old stage (human)" }, "devStageAuthorAnnotation": "60-64 (64 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 216.543957, "sdRefIntergenicDistribution": 1.120046, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 4427, "distinctRankCount": 269, "maxRank": 18610.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 177386680, "mappedReadsCount": 99551829, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138845" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008952", "name": "upper lobe of left lung" }, "anatEntityAuthorAnnotation": "Upper left lobe", "cellType": { "id": "CL:0002144", "name": "capillary endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_Cap_a, Vascular", "devStage": { "id": "HsapDv:0000158", "name": "64-year-old stage (human)" }, "devStageAuthorAnnotation": "60-64 (64 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 62.369515, "sdRefIntergenicDistribution": 1.263623, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 16174, "distinctRankCount": 853, "maxRank": 19942.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 177386680, "mappedReadsCount": 99551829, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138845" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008952", "name": "upper lobe of left lung" }, "anatEntityAuthorAnnotation": "Upper left lobe", "cellType": { "id": "CL:0002144", "name": "capillary endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_Cap_g, Vascular", "devStage": { "id": "HsapDv:0000158", "name": "64-year-old stage (human)" }, "devStageAuthorAnnotation": "60-64 (64 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 18.971164, "sdRefIntergenicDistribution": 1.400999, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 56027, "distinctRankCount": 1810, "maxRank": 22086.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 177386680, "mappedReadsCount": 99551829, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138845" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008952", "name": "upper lobe of left lung" }, "anatEntityAuthorAnnotation": "Upper left lobe", "cellType": { "id": "CL:0002553", "name": "fibroblast of lung" }, "cellTypeAuthorAnnotation": "Fibro_adventitial, Stroma", "devStage": { "id": "HsapDv:0000158", "name": "64-year-old stage (human)" }, "devStageAuthorAnnotation": "60-64 (64 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 35.830361, "sdRefIntergenicDistribution": 1.289880, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 28102, "distinctRankCount": 1365, "maxRank": 20835.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 177386680, "mappedReadsCount": 99551829, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138845" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008952", "name": "upper lobe of left lung" }, "anatEntityAuthorAnnotation": "Upper left lobe", "cellType": { "id": "CL:0002553", "name": "fibroblast of lung" }, "cellTypeAuthorAnnotation": "Fibro_alveolar, Stroma", "devStage": { "id": "HsapDv:0000158", "name": "64-year-old stage (human)" }, "devStageAuthorAnnotation": "60-64 (64 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 3.271987, "sdRefIntergenicDistribution": 1.923736, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 442338, "distinctRankCount": 3568, "maxRank": 25374.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 177386680, "mappedReadsCount": 99551829, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138845" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008952", "name": "upper lobe of left lung" }, "anatEntityAuthorAnnotation": "Upper left lobe", "cellType": { "id": "CL:0002553", "name": "fibroblast of lung" }, "cellTypeAuthorAnnotation": "Fibro_peribronchial, Stroma", "devStage": { "id": "HsapDv:0000158", "name": "64-year-old stage (human)" }, "devStageAuthorAnnotation": "60-64 (64 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 66.979050, "sdRefIntergenicDistribution": 1.251387, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 14794, "distinctRankCount": 951, "maxRank": 19893.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 177386680, "mappedReadsCount": 99551829, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138845" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008952", "name": "upper lobe of left lung" }, "anatEntityAuthorAnnotation": "Upper left lobe", "cellType": { "id": "CL:0002553", "name": "fibroblast of lung" }, "cellTypeAuthorAnnotation": "Fibro_perichondrial, Stroma", "devStage": { "id": "HsapDv:0000158", "name": "64-year-old stage (human)" }, "devStageAuthorAnnotation": "60-64 (64 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 267.005804, "sdRefIntergenicDistribution": 1.303431, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 3771, "distinctRankCount": 281, "maxRank": 18376.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 177386680, "mappedReadsCount": 99551829, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138845" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008952", "name": "upper lobe of left lung" }, "anatEntityAuthorAnnotation": "Upper left lobe", "cellType": { "id": "CL:0002543", "name": "vein endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_venous_pulmonary, Vascular", "devStage": { "id": "HsapDv:0000158", "name": "64-year-old stage (human)" }, "devStageAuthorAnnotation": "60-64 (64 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 34.474292, "sdRefIntergenicDistribution": 1.351874, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 30296, "distinctRankCount": 1393, "maxRank": 20819.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 177386680, "mappedReadsCount": 99551829, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138845" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008952", "name": "upper lobe of left lung" }, "anatEntityAuthorAnnotation": "Upper left lobe", "cellType": { "id": "CL:0002543", "name": "vein endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_venous_systemic, Vascular", "devStage": { "id": "HsapDv:0000158", "name": "64-year-old stage (human)" }, "devStageAuthorAnnotation": "60-64 (64 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 60.714520, "sdRefIntergenicDistribution": 1.272196, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 16604, "distinctRankCount": 1154, "maxRank": 19874.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 177386680, "mappedReadsCount": 99551829, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138845" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008952", "name": "upper lobe of left lung" }, "anatEntityAuthorAnnotation": "Upper left lobe", "cellType": { "id": "CL:0000160", "name": "goblet cell" }, "cellTypeAuthorAnnotation": "Secretory_Goblet, Epithelia", "devStage": { "id": "HsapDv:0000158", "name": "64-year-old stage (human)" }, "devStageAuthorAnnotation": "60-64 (64 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 6.336664, "sdRefIntergenicDistribution": 1.688669, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 195665, "distinctRankCount": 3051, "maxRank": 23790.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 177386680, "mappedReadsCount": 99551829, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138845" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008952", "name": "upper lobe of left lung" }, "anatEntityAuthorAnnotation": "Upper left lobe", "cellType": { "id": "CL:0002063", "name": "type II pneumocyte" }, "cellTypeAuthorAnnotation": "AT2, Epithelia", "devStage": { "id": "HsapDv:0000158", "name": "64-year-old stage (human)" }, "devStageAuthorAnnotation": "60-64 (64 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 0.905480, "sdRefIntergenicDistribution": 2.730876, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 3667288, "distinctRankCount": 6022, "maxRank": 27568.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 177386680, "mappedReadsCount": 99551829, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138845" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008952", "name": "upper lobe of left lung" }, "anatEntityAuthorAnnotation": "Upper left lobe", "cellType": { "id": "CL:0002063", "name": "type II pneumocyte" }, "cellTypeAuthorAnnotation": "Dividing_AT2, Epithelia", "devStage": { "id": "HsapDv:0000158", "name": "64-year-old stage (human)" }, "devStageAuthorAnnotation": "60-64 (64 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 23.937046, "sdRefIntergenicDistribution": 1.448996, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 45092, "distinctRankCount": 1987, "maxRank": 21174.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 177386680, "mappedReadsCount": 99551829, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138845" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008952", "name": "upper lobe of left lung" }, "anatEntityAuthorAnnotation": "Upper left lobe", "cellType": { "id": "CL:0000583", "name": "alveolar macrophage" }, "cellTypeAuthorAnnotation": "Macro_alveolar, Immune", "devStage": { "id": "HsapDv:0000158", "name": "64-year-old stage (human)" }, "devStageAuthorAnnotation": "60-64 (64 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 1.380201, "sdRefIntergenicDistribution": 2.446609, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1646414, "distinctRankCount": 5113, "maxRank": 26722.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 177386680, "mappedReadsCount": 99551829, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138845" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008952", "name": "upper lobe of left lung" }, "anatEntityAuthorAnnotation": "Upper left lobe", "cellType": { "id": "CL:0000583", "name": "alveolar macrophage" }, "cellTypeAuthorAnnotation": "Macro_alveolar_metallothioneins, Immune", "devStage": { "id": "HsapDv:0000158", "name": "64-year-old stage (human)" }, "devStageAuthorAnnotation": "60-64 (64 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 297.124571, "sdRefIntergenicDistribution": 1.142702, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 3222, "distinctRankCount": 227, "maxRank": 18422.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 177386680, "mappedReadsCount": 99551829, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138845" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008952", "name": "upper lobe of left lung" }, "anatEntityAuthorAnnotation": "Upper left lobe", "cellType": { "id": "CL:0000319", "name": "mucus secreting cell" }, "cellTypeAuthorAnnotation": "SMG_Mucous, Epithelia", "devStage": { "id": "HsapDv:0000158", "name": "64-year-old stage (human)" }, "devStageAuthorAnnotation": "60-64 (64 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 21.264737, "sdRefIntergenicDistribution": 1.438474, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 50411, "distinctRankCount": 1661, "maxRank": 21701.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 177386680, "mappedReadsCount": 99551829, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138845" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008952", "name": "upper lobe of left lung" }, "anatEntityAuthorAnnotation": "Upper left lobe", "cellType": { "id": "CL:0009115", "name": "lymph node lymphatic vessel endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_Lymphatic, Vascular", "devStage": { "id": "HsapDv:0000158", "name": "64-year-old stage (human)" }, "devStageAuthorAnnotation": "60-64 (64 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 7.964079, "sdRefIntergenicDistribution": 1.624210, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 147169, "distinctRankCount": 2947, "maxRank": 23511.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 177386680, "mappedReadsCount": 99551829, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138845" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008952", "name": "upper lobe of left lung" }, "anatEntityAuthorAnnotation": "Upper left lobe", "cellType": { "id": "CL:0000158", "name": "club cell" }, "cellTypeAuthorAnnotation": "Secretory_Club, Epithelia", "devStage": { "id": "HsapDv:0000158", "name": "64-year-old stage (human)" }, "devStageAuthorAnnotation": "60-64 (64 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 2.792373, "sdRefIntergenicDistribution": 1.945905, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 544150, "distinctRankCount": 3819, "maxRank": 25484.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 177386680, "mappedReadsCount": 99551829, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138845" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008952", "name": "upper lobe of left lung" }, "anatEntityAuthorAnnotation": "Upper left lobe", "cellType": { "id": "CL:0000077", "name": "mesothelial cell" }, "cellTypeAuthorAnnotation": "Mesothelia, Stroma", "devStage": { "id": "HsapDv:0000158", "name": "64-year-old stage (human)" }, "devStageAuthorAnnotation": "60-64 (64 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 511.692985, "sdRefIntergenicDistribution": 1.123279, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1852, "distinctRankCount": 142, "maxRank": 18144.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 177386680, "mappedReadsCount": 99551829, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138845" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008952", "name": "upper lobe of left lung" }, "anatEntityAuthorAnnotation": "Upper left lobe", "cellType": { "id": "CL:0002633", "name": "respiratory basal cell" }, "cellTypeAuthorAnnotation": "Basal, Epithelia", "devStage": { "id": "HsapDv:0000158", "name": "64-year-old stage (human)" }, "devStageAuthorAnnotation": "60-64 (64 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 24.003660, "sdRefIntergenicDistribution": 1.389869, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 43737, "distinctRankCount": 1879, "maxRank": 21570.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 177386680, "mappedReadsCount": 99551829, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138845" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008952", "name": "upper lobe of left lung" }, "anatEntityAuthorAnnotation": "Upper left lobe", "cellType": { "id": "CL:0002633", "name": "respiratory basal cell" }, "cellTypeAuthorAnnotation": "Dividing_Basal, Epithelia", "devStage": { "id": "HsapDv:0000158", "name": "64-year-old stage (human)" }, "devStageAuthorAnnotation": "60-64 (64 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 73.290186, "sdRefIntergenicDistribution": 1.273238, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 13579, "distinctRankCount": 1100, "maxRank": 19639.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 177386680, "mappedReadsCount": 99551829, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138845" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008952", "name": "upper lobe of left lung" }, "anatEntityAuthorAnnotation": "Upper left lobe", "cellType": { "id": "CL:0002633", "name": "respiratory basal cell" }, "cellTypeAuthorAnnotation": "SMG_Basal, Epithelia", "devStage": { "id": "HsapDv:0000158", "name": "64-year-old stage (human)" }, "devStageAuthorAnnotation": "60-64 (64 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 863.084922, "sdRefIntergenicDistribution": 1.270186, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1089, "distinctRankCount": 72, "maxRank": 17921.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 177386680, "mappedReadsCount": 99551829, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138845" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008952", "name": "upper lobe of left lung" }, "anatEntityAuthorAnnotation": "Upper left lobe", "cellType": { "id": "CL:0002368", "name": "respiratory epithelial cell" }, "cellTypeAuthorAnnotation": "Suprabasal, Epithelia", "devStage": { "id": "HsapDv:0000158", "name": "64-year-old stage (human)" }, "devStageAuthorAnnotation": "60-64 (64 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 23.339522, "sdRefIntergenicDistribution": 1.447787, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 45975, "distinctRankCount": 1919, "maxRank": 21312.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 177386680, "mappedReadsCount": 99551829, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138845" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008952", "name": "upper lobe of left lung" }, "anatEntityAuthorAnnotation": "Upper left lobe", "cellType": { "id": "CL:0000192", "name": "smooth muscle cell" }, "cellTypeAuthorAnnotation": "Muscle_smooth_pulmonary, Stroma", "devStage": { "id": "HsapDv:0000158", "name": "64-year-old stage (human)" }, "devStageAuthorAnnotation": "60-64 (64 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 73.649846, "sdRefIntergenicDistribution": 1.243841, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 13619, "distinctRankCount": 776, "maxRank": 19661.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 177386680, "mappedReadsCount": 99551829, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138845" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008952", "name": "upper lobe of left lung" }, "anatEntityAuthorAnnotation": "Upper left lobe", "cellType": { "id": "CL:0000146", "name": "simple columnar epithelial cell" }, "cellTypeAuthorAnnotation": "SMG_Duct, Epithelia", "devStage": { "id": "HsapDv:0000158", "name": "64-year-old stage (human)" }, "devStageAuthorAnnotation": "60-64 (64 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 12.981802, "sdRefIntergenicDistribution": 1.508499, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 86853, "distinctRankCount": 2387, "maxRank": 22377.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 177386680, "mappedReadsCount": 99551829, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138845" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008952", "name": "upper lobe of left lung" }, "anatEntityAuthorAnnotation": "Upper left lobe", "cellType": { "id": "CL:0000623", "name": "natural killer cell" }, "cellTypeAuthorAnnotation": "NK_CD11d, Immune", "devStage": { "id": "HsapDv:0000158", "name": "64-year-old stage (human)" }, "devStageAuthorAnnotation": "60-64 (64 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 1914.866059, "sdRefIntergenicDistribution": 1.167502, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 493, "distinctRankCount": 12, "maxRank": 17750.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 177386680, "mappedReadsCount": 99551829, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138845" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008952", "name": "upper lobe of left lung" }, "anatEntityAuthorAnnotation": "Upper left lobe", "cellType": { "id": "CL:0000623", "name": "natural killer cell" }, "cellTypeAuthorAnnotation": "NK_CD16hi, Immune", "devStage": { "id": "HsapDv:0000158", "name": "64-year-old stage (human)" }, "devStageAuthorAnnotation": "60-64 (64 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 428.228925, "sdRefIntergenicDistribution": 1.229988, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 2274, "distinctRankCount": 170, "maxRank": 18232.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 177386680, "mappedReadsCount": 99551829, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138845" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008952", "name": "upper lobe of left lung" }, "anatEntityAuthorAnnotation": "Upper left lobe", "cellType": { "id": "CL:1001568", "name": "pulmonary artery endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_arterial_pulmonary, Vascular", "devStage": { "id": "HsapDv:0000158", "name": "64-year-old stage (human)" }, "devStageAuthorAnnotation": "60-64 (64 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 17.273652, "sdRefIntergenicDistribution": 1.498842, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 63437, "distinctRankCount": 1968, "maxRank": 21941.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 177386680, "mappedReadsCount": 99551829, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138845" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008952", "name": "upper lobe of left lung" }, "anatEntityAuthorAnnotation": "Upper left lobe", "cellType": { "id": "CL:1001603", "name": "lung macrophage" }, "cellTypeAuthorAnnotation": "Macro_CCL, Immune", "devStage": { "id": "HsapDv:0000158", "name": "64-year-old stage (human)" }, "devStageAuthorAnnotation": "60-64 (64 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 160.446467, "sdRefIntergenicDistribution": 1.274036, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 6330, "distinctRankCount": 429, "maxRank": 18833.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 177386680, "mappedReadsCount": 99551829, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138845" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008952", "name": "upper lobe of left lung" }, "anatEntityAuthorAnnotation": "Upper left lobe", "cellType": { "id": "CL:1001603", "name": "lung macrophage" }, "cellTypeAuthorAnnotation": "Macro_CHIT1, Immune", "devStage": { "id": "HsapDv:0000158", "name": "64-year-old stage (human)" }, "devStageAuthorAnnotation": "60-64 (64 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 56.503013, "sdRefIntergenicDistribution": 1.338130, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 18178, "distinctRankCount": 1112, "maxRank": 20033.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 177386680, "mappedReadsCount": 99551829, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138845" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008952", "name": "upper lobe of left lung" }, "anatEntityAuthorAnnotation": "Upper left lobe", "cellType": { "id": "CL:1001603", "name": "lung macrophage" }, "cellTypeAuthorAnnotation": "Macro_dividing, Immune", "devStage": { "id": "HsapDv:0000158", "name": "64-year-old stage (human)" }, "devStageAuthorAnnotation": "60-64 (64 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 28.424752, "sdRefIntergenicDistribution": 1.429842, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 37483, "distinctRankCount": 1775, "maxRank": 20953.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 177386680, "mappedReadsCount": 99551829, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138845" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008952", "name": "upper lobe of left lung" }, "anatEntityAuthorAnnotation": "Upper left lobe", "cellType": { "id": "CL:1001603", "name": "lung macrophage" }, "cellTypeAuthorAnnotation": "Macro_intermediate, Immune", "devStage": { "id": "HsapDv:0000158", "name": "64-year-old stage (human)" }, "devStageAuthorAnnotation": "60-64 (64 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 1947.363310, "sdRefIntergenicDistribution": 1.002496, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 477, "distinctRankCount": 24, "maxRank": 17755.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 177386680, "mappedReadsCount": 99551829, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138845" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008952", "name": "upper lobe of left lung" }, "anatEntityAuthorAnnotation": "Upper left lobe", "cellType": { "id": "CL:1001603", "name": "lung macrophage" }, "cellTypeAuthorAnnotation": "Macro_interstitial, Immune", "devStage": { "id": "HsapDv:0000158", "name": "64-year-old stage (human)" }, "devStageAuthorAnnotation": "60-64 (64 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 164.050145, "sdRefIntergenicDistribution": 1.224055, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 6015, "distinctRankCount": 593, "maxRank": 18738.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 177386680, "mappedReadsCount": 99551829, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138845" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008952", "name": "upper lobe of left lung" }, "anatEntityAuthorAnnotation": "Upper left lobe", "cellType": { "id": "CL:1001603", "name": "lung macrophage" }, "cellTypeAuthorAnnotation": "Macro_intravascular, Immune", "devStage": { "id": "HsapDv:0000158", "name": "64-year-old stage (human)" }, "devStageAuthorAnnotation": "60-64 (64 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 256.951819, "sdRefIntergenicDistribution": 1.198878, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 3836, "distinctRankCount": 284, "maxRank": 18507.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 177386680, "mappedReadsCount": 99551829, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138845" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008952", "name": "upper lobe of left lung" }, "anatEntityAuthorAnnotation": "Upper left lobe", "cellType": { "id": "CL:1000413", "name": "endothelial cell of artery" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_arterial_systemic, Vascular", "devStage": { "id": "HsapDv:0000158", "name": "64-year-old stage (human)" }, "devStageAuthorAnnotation": "60-64 (64 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 350.966271, "sdRefIntergenicDistribution": 1.219299, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 2829, "distinctRankCount": 184, "maxRank": 18317.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 177386680, "mappedReadsCount": 99551829, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138845" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008952", "name": "upper lobe of left lung" }, "anatEntityAuthorAnnotation": "Upper left lobe", "cellType": { "id": "CL:0000624", "name": "CD4-positive, alpha-beta T cell" }, "cellTypeAuthorAnnotation": "CD4_EM/Effector, Immune", "devStage": { "id": "HsapDv:0000158", "name": "64-year-old stage (human)" }, "devStageAuthorAnnotation": "60-64 (64 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 208.179019, "sdRefIntergenicDistribution": 1.183265, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 4632, "distinctRankCount": 275, "maxRank": 18753.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 177386680, "mappedReadsCount": 99551829, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138845" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008952", "name": "upper lobe of left lung" }, "anatEntityAuthorAnnotation": "Upper left lobe", "cellType": { "id": "CL:0000624", "name": "CD4-positive, alpha-beta T cell" }, "cellTypeAuthorAnnotation": "CD4_naive/CM, Immune", "devStage": { "id": "HsapDv:0000158", "name": "64-year-old stage (human)" }, "devStageAuthorAnnotation": "60-64 (64 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 391.029139, "sdRefIntergenicDistribution": 1.183646, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 2448, "distinctRankCount": 160, "maxRank": 18262.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 177386680, "mappedReadsCount": 99551829, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138845" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008952", "name": "upper lobe of left lung" }, "anatEntityAuthorAnnotation": "Upper left lobe", "cellType": { "id": "CL:4033044", "name": "deuterosomal cell" }, "cellTypeAuthorAnnotation": "Deuterosomal, Epithelia", "devStage": { "id": "HsapDv:0000158", "name": "64-year-old stage (human)" }, "devStageAuthorAnnotation": "60-64 (64 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 162.731192, "sdRefIntergenicDistribution": 1.232959, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 6123, "distinctRankCount": 593, "maxRank": 18676.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 177386680, "mappedReadsCount": 99551829, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138845" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008952", "name": "upper lobe of left lung" }, "anatEntityAuthorAnnotation": "Upper left lobe", "cellType": { "id": "CL:0000097", "name": "mast cell" }, "cellTypeAuthorAnnotation": "Mast_cell , Immune", "devStage": { "id": "HsapDv:0000158", "name": "64-year-old stage (human)" }, "devStageAuthorAnnotation": "60-64 (64 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 115.613123, "sdRefIntergenicDistribution": 1.249840, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 8505, "distinctRankCount": 521, "maxRank": 19276.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 177386680, "mappedReadsCount": 99551829, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138845" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008952", "name": "upper lobe of left lung" }, "anatEntityAuthorAnnotation": "Upper left lobe", "cellType": { "id": "CL:0000787", "name": "memory B cell" }, "cellTypeAuthorAnnotation": "B_memory, Immune", "devStage": { "id": "HsapDv:0000158", "name": "64-year-old stage (human)" }, "devStageAuthorAnnotation": "60-64 (64 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 337.985435, "sdRefIntergenicDistribution": 1.157516, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 2826, "distinctRankCount": 187, "maxRank": 18351.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 177386680, "mappedReadsCount": 99551829, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138845" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008952", "name": "upper lobe of left lung" }, "anatEntityAuthorAnnotation": "Upper left lobe", "cellType": { "id": "CL:0000186", "name": "myofibroblast cell" }, "cellTypeAuthorAnnotation": "Fibro_myofibroblast, Stroma", "devStage": { "id": "HsapDv:0000158", "name": "64-year-old stage (human)" }, "devStageAuthorAnnotation": "60-64 (64 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 130.013256, "sdRefIntergenicDistribution": 1.171547, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 7402, "distinctRankCount": 561, "maxRank": 18974.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 177386680, "mappedReadsCount": 99551829, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138845" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008952", "name": "upper lobe of left lung" }, "anatEntityAuthorAnnotation": "Upper left lobe", "cellType": { "id": "CL:0009089", "name": "lung pericyte" }, "cellTypeAuthorAnnotation": "Muscle_pericyte_pulmonary, Stroma", "devStage": { "id": "HsapDv:0000158", "name": "64-year-old stage (human)" }, "devStageAuthorAnnotation": "60-64 (64 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 109.660237, "sdRefIntergenicDistribution": 1.209240, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 8997, "distinctRankCount": 600, "maxRank": 19195.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 177386680, "mappedReadsCount": 99551829, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138845" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008952", "name": "upper lobe of left lung" }, "anatEntityAuthorAnnotation": "Upper left lobe", "cellType": { "id": "CL:0000784", "name": "plasmacytoid dendritic cell" }, "cellTypeAuthorAnnotation": "DC_plasmacytoid, Immune", "devStage": { "id": "HsapDv:0000158", "name": "64-year-old stage (human)" }, "devStageAuthorAnnotation": "60-64 (64 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 169.102027, "sdRefIntergenicDistribution": 1.285678, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 5962, "distinctRankCount": 607, "maxRank": 18746.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 177386680, "mappedReadsCount": 99551829, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138845" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008952", "name": "upper lobe of left lung" }, "anatEntityAuthorAnnotation": "Upper left lobe", "cellType": { "id": "CL:0000990", "name": "conventional dendritic cell" }, "cellTypeAuthorAnnotation": "DC_2, Immune", "devStage": { "id": "HsapDv:0000158", "name": "64-year-old stage (human)" }, "devStageAuthorAnnotation": "60-64 (64 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 1429.432138, "sdRefIntergenicDistribution": 1.231461, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 693, "distinctRankCount": 40, "maxRank": 17783.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 177386680, "mappedReadsCount": 99551829, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138845" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008952", "name": "upper lobe of left lung" }, "anatEntityAuthorAnnotation": "Upper left lobe", "cellType": { "id": "CL:0000057", "name": "fibroblast" }, "cellTypeAuthorAnnotation": "NAF_perineurial, Stroma", "devStage": { "id": "HsapDv:0000158", "name": "64-year-old stage (human)" }, "devStageAuthorAnnotation": "60-64 (64 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 1809.996261, "sdRefIntergenicDistribution": 1.001996, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 525, "distinctRankCount": 42, "maxRank": 17761.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 177386680, "mappedReadsCount": 99551829, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138845" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008952", "name": "upper lobe of left lung" }, "anatEntityAuthorAnnotation": "Upper left lobe", "cellType": { "id": "CL:0000138", "name": "chondrocyte" }, "cellTypeAuthorAnnotation": "Chondrocyte, Stroma", "devStage": { "id": "HsapDv:0000158", "name": "64-year-old stage (human)" }, "devStageAuthorAnnotation": "60-64 (64 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 73.441449, "sdRefIntergenicDistribution": 1.314860, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 13791, "distinctRankCount": 1046, "maxRank": 19581.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 177386680, "mappedReadsCount": 99551829, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138845" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008952", "name": "upper lobe of left lung" }, "anatEntityAuthorAnnotation": "Upper left lobe", "cellType": { "id": "CL:0000987", "name": "IgA plasma cell" }, "cellTypeAuthorAnnotation": "B_plasma_IgA, Immune", "devStage": { "id": "HsapDv:0000158", "name": "64-year-old stage (human)" }, "devStageAuthorAnnotation": "60-64 (64 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 326.632170, "sdRefIntergenicDistribution": 1.143348, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 2933, "distinctRankCount": 171, "maxRank": 18288.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 177386680, "mappedReadsCount": 99551829, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138845" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008952", "name": "upper lobe of left lung" }, "anatEntityAuthorAnnotation": "Upper left lobe", "cellType": { "id": "CL:0000985", "name": "IgG plasma cell" }, "cellTypeAuthorAnnotation": "B_plasma_IgG, Immune", "devStage": { "id": "HsapDv:0000158", "name": "64-year-old stage (human)" }, "devStageAuthorAnnotation": "60-64 (64 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 534.539482, "sdRefIntergenicDistribution": 1.125303, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1754, "distinctRankCount": 125, "maxRank": 18107.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 177386680, "mappedReadsCount": 99551829, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138845" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008952", "name": "upper lobe of left lung" }, "anatEntityAuthorAnnotation": "Upper left lobe", "cellType": { "id": "CL:0001054", "name": "CD14-positive monocyte" }, "cellTypeAuthorAnnotation": "Monocyte_CD14, Immune", "devStage": { "id": "HsapDv:0000158", "name": "64-year-old stage (human)" }, "devStageAuthorAnnotation": "60-64 (64 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 2136.751908, "sdRefIntergenicDistribution": 1.000000, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 0, "distinctRankCount": 0 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 177386680, "mappedReadsCount": 99551829, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138845" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008952", "name": "upper lobe of left lung" }, "anatEntityAuthorAnnotation": "Upper left lobe", "cellType": { "id": "CL:0000556", "name": "megakaryocyte" }, "cellTypeAuthorAnnotation": "Megakaryocyte, Immune", "devStage": { "id": "HsapDv:0000158", "name": "64-year-old stage (human)" }, "devStageAuthorAnnotation": "60-64 (64 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 399.793245, "sdRefIntergenicDistribution": 1.598057, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 2783, "distinctRankCount": 211, "maxRank": 18043.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 177386680, "mappedReadsCount": 99551829, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138845" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008952", "name": "upper lobe of left lung" }, "anatEntityAuthorAnnotation": "Upper left lobe", "cellType": { "id": "CL:0019019", "name": "tracheobronchial smooth muscle cell" }, "cellTypeAuthorAnnotation": "Muscle_smooth_airway, Stroma", "devStage": { "id": "HsapDv:0000158", "name": "64-year-old stage (human)" }, "devStageAuthorAnnotation": "60-64 (64 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 410.675917, "sdRefIntergenicDistribution": 1.137251, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 2367, "distinctRankCount": 155, "maxRank": 18090.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937709576, "mappedReadsCount": 568736953, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138850" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002144", "name": "capillary endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_Cap_a, Vascular", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 30.554965, "sdRefIntergenicDistribution": 1.375107, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 34000, "distinctRankCount": 1297, "maxRank": 21072.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937709576, "mappedReadsCount": 568736953, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138850" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002144", "name": "capillary endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_Cap_g, Vascular", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 14.510259, "sdRefIntergenicDistribution": 1.459859, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 74559, "distinctRankCount": 2017, "maxRank": 22331.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937709576, "mappedReadsCount": 568736953, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138850" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000067", "name": "ciliated epithelial cell" }, "cellTypeAuthorAnnotation": "Ciliated, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 40.864094, "sdRefIntergenicDistribution": 1.615188, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 28137, "distinctRankCount": 1511, "maxRank": 20541.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937709576, "mappedReadsCount": 568736953, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138850" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002396", "name": "CD14-low, CD16-positive monocyte" }, "cellTypeAuthorAnnotation": "Monocyte_CD16, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 34.181689, "sdRefIntergenicDistribution": 1.337855, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 29687, "distinctRankCount": 1201, "maxRank": 20711.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937709576, "mappedReadsCount": 568736953, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138850" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000909", "name": "CD8-positive, alpha-beta memory T cell" }, "cellTypeAuthorAnnotation": "CD8_TRM, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 63.558151, "sdRefIntergenicDistribution": 1.255618, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 15738, "distinctRankCount": 739, "maxRank": 19884.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937709576, "mappedReadsCount": 568736953, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138850" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000909", "name": "CD8-positive, alpha-beta memory T cell" }, "cellTypeAuthorAnnotation": "CD8_TRM/EM, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 38.875121, "sdRefIntergenicDistribution": 1.378381, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 26942, "distinctRankCount": 1079, "maxRank": 20541.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937709576, "mappedReadsCount": 568736953, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138850" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000897", "name": "CD4-positive, alpha-beta memory T cell" }, "cellTypeAuthorAnnotation": "CD4_TRM, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 57.124163, "sdRefIntergenicDistribution": 1.305835, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 17715, "distinctRankCount": 748, "maxRank": 19983.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937709576, "mappedReadsCount": 568736953, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138850" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000146", "name": "simple columnar epithelial cell" }, "cellTypeAuthorAnnotation": "SMG_Duct, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 47.107501, "sdRefIntergenicDistribution": 1.309799, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 21163, "distinctRankCount": 1193, "maxRank": 20279.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937709576, "mappedReadsCount": 568736953, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138850" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000097", "name": "mast cell" }, "cellTypeAuthorAnnotation": "Mast_cell , Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 29.767266, "sdRefIntergenicDistribution": 1.431387, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 34934, "distinctRankCount": 1350, "maxRank": 20819.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937709576, "mappedReadsCount": 568736953, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138850" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002633", "name": "respiratory basal cell" }, "cellTypeAuthorAnnotation": "Basal, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 3.592534, "sdRefIntergenicDistribution": 1.843854, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 392272, "distinctRankCount": 3648, "maxRank": 25227.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937709576, "mappedReadsCount": 568736953, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138850" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002633", "name": "respiratory basal cell" }, "cellTypeAuthorAnnotation": "Dividing_Basal, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 13.055709, "sdRefIntergenicDistribution": 1.470060, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 85093, "distinctRankCount": 2541, "maxRank": 22527.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937709576, "mappedReadsCount": 568736953, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138850" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002633", "name": "respiratory basal cell" }, "cellTypeAuthorAnnotation": "SMG_Basal, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 69.992531, "sdRefIntergenicDistribution": 1.327241, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 14571, "distinctRankCount": 779, "maxRank": 19616.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937709576, "mappedReadsCount": 568736953, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138850" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000624", "name": "CD4-positive, alpha-beta T cell" }, "cellTypeAuthorAnnotation": "CD4_EM/Effector, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 9.075824, "sdRefIntergenicDistribution": 1.531152, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 127029, "distinctRankCount": 2135, "maxRank": 23353.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937709576, "mappedReadsCount": 568736953, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138850" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000624", "name": "CD4-positive, alpha-beta T cell" }, "cellTypeAuthorAnnotation": "CD4_naive/CM, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 15.012577, "sdRefIntergenicDistribution": 1.442216, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 72156, "distinctRankCount": 1705, "maxRank": 22243.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937709576, "mappedReadsCount": 568736953, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138850" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000583", "name": "alveolar macrophage" }, "cellTypeAuthorAnnotation": "Macro_alveolar, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 5.056725, "sdRefIntergenicDistribution": 1.713679, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 252963, "distinctRankCount": 3274, "maxRank": 24061.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937709576, "mappedReadsCount": 568736953, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138850" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000583", "name": "alveolar macrophage" }, "cellTypeAuthorAnnotation": "Macro_alveolar_metallothioneins, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 43.596148, "sdRefIntergenicDistribution": 1.320650, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 23126, "distinctRankCount": 1029, "maxRank": 20199.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937709576, "mappedReadsCount": 568736953, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138850" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000815", "name": "regulatory T cell" }, "cellTypeAuthorAnnotation": "T_reg, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 43.959203, "sdRefIntergenicDistribution": 1.301979, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 22522, "distinctRankCount": 1000, "maxRank": 20422.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937709576, "mappedReadsCount": 568736953, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138850" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002553", "name": "fibroblast of lung" }, "cellTypeAuthorAnnotation": "Fibro_adventitial, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 5.490076, "sdRefIntergenicDistribution": 1.694025, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 233197, "distinctRankCount": 3010, "maxRank": 24288.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937709576, "mappedReadsCount": 568736953, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138850" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002553", "name": "fibroblast of lung" }, "cellTypeAuthorAnnotation": "Fibro_alveolar, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 3.289585, "sdRefIntergenicDistribution": 1.946324, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 461244, "distinctRankCount": 3703, "maxRank": 25528.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937709576, "mappedReadsCount": 568736953, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138850" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002553", "name": "fibroblast of lung" }, "cellTypeAuthorAnnotation": "Fibro_peribronchial, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 12.734381, "sdRefIntergenicDistribution": 1.454438, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 85377, "distinctRankCount": 2147, "maxRank": 22409.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937709576, "mappedReadsCount": 568736953, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138850" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002553", "name": "fibroblast of lung" }, "cellTypeAuthorAnnotation": "Fibro_perichondrial, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 104.444366, "sdRefIntergenicDistribution": 1.254756, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 9540, "distinctRankCount": 568, "maxRank": 19183.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937709576, "mappedReadsCount": 568736953, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138850" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:1001603", "name": "lung macrophage" }, "cellTypeAuthorAnnotation": "Macro_CCL, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 590.959877, "sdRefIntergenicDistribution": 1.182512, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1602, "distinctRankCount": 81, "maxRank": 17922.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937709576, "mappedReadsCount": 568736953, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138850" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:1001603", "name": "lung macrophage" }, "cellTypeAuthorAnnotation": "Macro_CHIT1, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 102.558960, "sdRefIntergenicDistribution": 1.344020, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 9604, "distinctRankCount": 789, "maxRank": 19293.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937709576, "mappedReadsCount": 568736953, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138850" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:1001603", "name": "lung macrophage" }, "cellTypeAuthorAnnotation": "Macro_intermediate, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 38.950004, "sdRefIntergenicDistribution": 1.305185, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 26149, "distinctRankCount": 1241, "maxRank": 20313.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937709576, "mappedReadsCount": 568736953, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138850" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:1001603", "name": "lung macrophage" }, "cellTypeAuthorAnnotation": "Macro_interstitial, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 769.424184, "sdRefIntergenicDistribution": 1.113451, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1081, "distinctRankCount": 49, "maxRank": 17874.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937709576, "mappedReadsCount": 568736953, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138850" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:1001603", "name": "lung macrophage" }, "cellTypeAuthorAnnotation": "Macro_intravascular, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 98.105837, "sdRefIntergenicDistribution": 1.301252, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 9976, "distinctRankCount": 518, "maxRank": 19238.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937709576, "mappedReadsCount": 568736953, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138850" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000623", "name": "natural killer cell" }, "cellTypeAuthorAnnotation": "NK_CD11d, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 338.394784, "sdRefIntergenicDistribution": 1.209982, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 2932, "distinctRankCount": 152, "maxRank": 18336.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937709576, "mappedReadsCount": 568736953, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138850" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000623", "name": "natural killer cell" }, "cellTypeAuthorAnnotation": "NK_CD16hi, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 10.559005, "sdRefIntergenicDistribution": 1.517751, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 106602, "distinctRankCount": 2062, "maxRank": 23072.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937709576, "mappedReadsCount": 568736953, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138850" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000985", "name": "IgG plasma cell" }, "cellTypeAuthorAnnotation": "B_plasma_IgG, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 116.690381, "sdRefIntergenicDistribution": 1.333678, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 8781, "distinctRankCount": 461, "maxRank": 18880.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937709576, "mappedReadsCount": 568736953, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138850" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0009115", "name": "lymph node lymphatic vessel endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_Lymphatic, Vascular", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 6.303660, "sdRefIntergenicDistribution": 1.640201, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 186763, "distinctRankCount": 3245, "maxRank": 24324.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937709576, "mappedReadsCount": 568736953, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138850" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000913", "name": "effector memory CD8-positive, alpha-beta T cell" }, "cellTypeAuthorAnnotation": "CD8_EM, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 32.596752, "sdRefIntergenicDistribution": 1.328185, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 31655, "distinctRankCount": 1184, "maxRank": 20738.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937709576, "mappedReadsCount": 568736953, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138850" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000913", "name": "effector memory CD8-positive, alpha-beta T cell" }, "cellTypeAuthorAnnotation": "CD8_EM/EMRA, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 161.065498, "sdRefIntergenicDistribution": 1.290861, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 6226, "distinctRankCount": 322, "maxRank": 18834.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937709576, "mappedReadsCount": 568736953, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138850" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000186", "name": "myofibroblast cell" }, "cellTypeAuthorAnnotation": "Fibro_myofibroblast, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 71.652930, "sdRefIntergenicDistribution": 1.296248, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 13984, "distinctRankCount": 798, "maxRank": 19642.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937709576, "mappedReadsCount": 568736953, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138850" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000158", "name": "club cell" }, "cellTypeAuthorAnnotation": "Secretory_Club, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 23.542500, "sdRefIntergenicDistribution": 1.430101, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 44951, "distinctRankCount": 1769, "maxRank": 21139.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937709576, "mappedReadsCount": 568736953, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138850" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000192", "name": "smooth muscle cell" }, "cellTypeAuthorAnnotation": "Muscle_smooth_pulmonary, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 31.650326, "sdRefIntergenicDistribution": 1.355420, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 32327, "distinctRankCount": 1509, "maxRank": 21013.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937709576, "mappedReadsCount": 568736953, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138850" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0019001", "name": "tracheobronchial serous cell" }, "cellTypeAuthorAnnotation": "SMG_Serous, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 1185.092299, "sdRefIntergenicDistribution": 1.206746, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 838, "distinctRankCount": 33, "maxRank": 17835.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937709576, "mappedReadsCount": 568736953, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138850" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0019019", "name": "tracheobronchial smooth muscle cell" }, "cellTypeAuthorAnnotation": "Muscle_smooth_airway, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 386.258728, "sdRefIntergenicDistribution": 1.269937, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 2405, "distinctRankCount": 130, "maxRank": 18118.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937709576, "mappedReadsCount": 568736953, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138850" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000990", "name": "conventional dendritic cell" }, "cellTypeAuthorAnnotation": "DC_1, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 202.899484, "sdRefIntergenicDistribution": 1.327729, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 4988, "distinctRankCount": 255, "maxRank": 18427.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937709576, "mappedReadsCount": 568736953, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138850" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000990", "name": "conventional dendritic cell" }, "cellTypeAuthorAnnotation": "DC_2, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 66.506299, "sdRefIntergenicDistribution": 1.329448, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 15184, "distinctRankCount": 758, "maxRank": 19763.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937709576, "mappedReadsCount": 568736953, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138850" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000990", "name": "conventional dendritic cell" }, "cellTypeAuthorAnnotation": "DC_activated, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 835.118428, "sdRefIntergenicDistribution": 1.202397, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1146, "distinctRankCount": 90, "maxRank": 17899.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937709576, "mappedReadsCount": 568736953, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138850" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0019018", "name": "blood vessel smooth muscle cell" }, "cellTypeAuthorAnnotation": "Muscle_perivascular_immune_recruiting, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 115.474537, "sdRefIntergenicDistribution": 1.305892, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 8568, "distinctRankCount": 472, "maxRank": 19056.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937709576, "mappedReadsCount": 568736953, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138850" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0019018", "name": "blood vessel smooth muscle cell" }, "cellTypeAuthorAnnotation": "Muscle_smooth_arterial_systemic, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 77.336077, "sdRefIntergenicDistribution": 1.291861, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 13084, "distinctRankCount": 669, "maxRank": 19385.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937709576, "mappedReadsCount": 568736953, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138850" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0001054", "name": "CD14-positive monocyte" }, "cellTypeAuthorAnnotation": "Monocyte_CD14, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 19.259970, "sdRefIntergenicDistribution": 1.393618, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 54161, "distinctRankCount": 1638, "maxRank": 21832.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937709576, "mappedReadsCount": 568736953, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138850" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002063", "name": "type II pneumocyte" }, "cellTypeAuthorAnnotation": "AT2, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 0.974085, "sdRefIntergenicDistribution": 2.850615, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 4133153, "distinctRankCount": 6648, "maxRank": 27730.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937709576, "mappedReadsCount": 568736953, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138850" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002063", "name": "type II pneumocyte" }, "cellTypeAuthorAnnotation": "Dividing_AT2, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 178.977577, "sdRefIntergenicDistribution": 1.329250, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 5535, "distinctRankCount": 481, "maxRank": 18592.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937709576, "mappedReadsCount": 568736953, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138850" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002543", "name": "vein endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_venous_pulmonary, Vascular", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 64.396480, "sdRefIntergenicDistribution": 1.260833, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 15148, "distinctRankCount": 1045, "maxRank": 19578.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937709576, "mappedReadsCount": 568736953, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138850" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002543", "name": "vein endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_venous_systemic, Vascular", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 12.041617, "sdRefIntergenicDistribution": 1.483399, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 91969, "distinctRankCount": 2276, "maxRank": 22651.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937709576, "mappedReadsCount": 568736953, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138850" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0009089", "name": "lung pericyte" }, "cellTypeAuthorAnnotation": "Muscle_pericyte_pulmonary, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 79.096235, "sdRefIntergenicDistribution": 1.257421, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 12264, "distinctRankCount": 815, "maxRank": 19557.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937709576, "mappedReadsCount": 568736953, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138850" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000814", "name": "mature NK T cell" }, "cellTypeAuthorAnnotation": "NKT, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 70.527742, "sdRefIntergenicDistribution": 1.266820, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 14273, "distinctRankCount": 675, "maxRank": 19740.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937709576, "mappedReadsCount": 568736953, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138850" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000160", "name": "goblet cell" }, "cellTypeAuthorAnnotation": "Secretory_Goblet, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 13.330357, "sdRefIntergenicDistribution": 1.532325, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 84857, "distinctRankCount": 2339, "maxRank": 22145.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937709576, "mappedReadsCount": 568736953, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138850" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000940", "name": "mucosal invariant T cell" }, "cellTypeAuthorAnnotation": "MAIT, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 84.814596, "sdRefIntergenicDistribution": 1.277952, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 11709, "distinctRankCount": 552, "maxRank": 19516.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937709576, "mappedReadsCount": 568736953, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138850" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000319", "name": "mucus secreting cell" }, "cellTypeAuthorAnnotation": "SMG_Mucous, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 69.198865, "sdRefIntergenicDistribution": 1.369843, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 14693, "distinctRankCount": 814, "maxRank": 19781.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937709576, "mappedReadsCount": 568736953, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138850" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:1001568", "name": "pulmonary artery endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_arterial_pulmonary, Vascular", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 86.423201, "sdRefIntergenicDistribution": 1.261118, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 11128, "distinctRankCount": 715, "maxRank": 19383.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937709576, "mappedReadsCount": 568736953, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138850" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000185", "name": "myoepithelial cell" }, "cellTypeAuthorAnnotation": "Myoepithelial, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 170.112374, "sdRefIntergenicDistribution": 1.159541, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 5413, "distinctRankCount": 321, "maxRank": 18764.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937709576, "mappedReadsCount": 568736953, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138850" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000798", "name": "gamma-delta T cell" }, "cellTypeAuthorAnnotation": "gdT, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 343.477462, "sdRefIntergenicDistribution": 1.277121, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 2972, "distinctRankCount": 126, "maxRank": 18283.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937709576, "mappedReadsCount": 568736953, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138850" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000788", "name": "naive B cell" }, "cellTypeAuthorAnnotation": "B_naive, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 194.882734, "sdRefIntergenicDistribution": 1.222536, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 5008, "distinctRankCount": 248, "maxRank": 18566.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937709576, "mappedReadsCount": 568736953, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138850" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000987", "name": "IgA plasma cell" }, "cellTypeAuthorAnnotation": "B_plasma_IgA, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 61.975635, "sdRefIntergenicDistribution": 1.456333, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 17159, "distinctRankCount": 928, "maxRank": 19614.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937709576, "mappedReadsCount": 568736953, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138850" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000057", "name": "fibroblast" }, "cellTypeAuthorAnnotation": "NAF_endoneurial, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 499.878395, "sdRefIntergenicDistribution": 1.191115, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1919, "distinctRankCount": 119, "maxRank": 17978.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937709576, "mappedReadsCount": 568736953, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138850" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000057", "name": "fibroblast" }, "cellTypeAuthorAnnotation": "NAF_perineurial, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 188.314881, "sdRefIntergenicDistribution": 1.261825, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 5228, "distinctRankCount": 324, "maxRank": 18589.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937709576, "mappedReadsCount": 568736953, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138850" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002376", "name": "non-myelinating Schwann cell" }, "cellTypeAuthorAnnotation": "Schwann_nonmyelinating, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 440.758462, "sdRefIntergenicDistribution": 1.326973, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 2325, "distinctRankCount": 108, "maxRank": 18141.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937709576, "mappedReadsCount": 568736953, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138850" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000787", "name": "memory B cell" }, "cellTypeAuthorAnnotation": "B_memory, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 76.366929, "sdRefIntergenicDistribution": 1.245691, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 12694, "distinctRankCount": 689, "maxRank": 19677.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937709576, "mappedReadsCount": 568736953, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138850" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000138", "name": "chondrocyte" }, "cellTypeAuthorAnnotation": "Chondrocyte, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 3.693807, "sdRefIntergenicDistribution": 1.918974, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 406163, "distinctRankCount": 3886, "maxRank": 25135.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937709576, "mappedReadsCount": 568736953, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138850" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002368", "name": "respiratory epithelial cell" }, "cellTypeAuthorAnnotation": "Suprabasal, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 5.995723, "sdRefIntergenicDistribution": 1.687984, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 209572, "distinctRankCount": 3413, "maxRank": 24029.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937709576, "mappedReadsCount": 568736953, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138850" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:1000413", "name": "endothelial cell of artery" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_arterial_systemic, Vascular", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 223.881159, "sdRefIntergenicDistribution": 1.224719, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 3891, "distinctRankCount": 228, "maxRank": 18375.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937709576, "mappedReadsCount": 568736953, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138850" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002062", "name": "type I pneumocyte" }, "cellTypeAuthorAnnotation": "AT1 , Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 2.289835, "sdRefIntergenicDistribution": 2.181413, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 791577, "distinctRankCount": 4611, "maxRank": 25813.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937709576, "mappedReadsCount": 568736953, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138850" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000218", "name": "myelinating Schwann cell" }, "cellTypeAuthorAnnotation": "Schwann_Myelinating, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 590.204539, "sdRefIntergenicDistribution": 1.500853, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1803, "distinctRankCount": 83, "maxRank": 18025.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937709576, "mappedReadsCount": 568736953, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138850" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000669", "name": "pericyte cell" }, "cellTypeAuthorAnnotation": "Muscle_pericyte_systemic, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 66.076183, "sdRefIntergenicDistribution": 1.257865, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 15233, "distinctRankCount": 834, "maxRank": 19634.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937709576, "mappedReadsCount": 568736953, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138850" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000556", "name": "megakaryocyte" }, "cellTypeAuthorAnnotation": "Megakaryocyte, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 111.333635, "sdRefIntergenicDistribution": 1.535652, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 10355, "distinctRankCount": 359, "maxRank": 18608.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 966284236, "mappedReadsCount": 584006115, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138853" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002144", "name": "capillary endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_Cap_a, Vascular", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 30.270462, "sdRefIntergenicDistribution": 1.427133, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 35256, "distinctRankCount": 1236, "maxRank": 20879.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 966284236, "mappedReadsCount": 584006115, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138853" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002144", "name": "capillary endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_Cap_g, Vascular", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 13.331837, "sdRefIntergenicDistribution": 1.479926, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 83208, "distinctRankCount": 1912, "maxRank": 22483.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 966284236, "mappedReadsCount": 584006115, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138853" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000067", "name": "ciliated epithelial cell" }, "cellTypeAuthorAnnotation": "Ciliated, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 26.047757, "sdRefIntergenicDistribution": 1.707649, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 45054, "distinctRankCount": 1881, "maxRank": 21194.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 966284236, "mappedReadsCount": 584006115, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138853" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002396", "name": "CD14-low, CD16-positive monocyte" }, "cellTypeAuthorAnnotation": "Monocyte_CD16, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 28.031737, "sdRefIntergenicDistribution": 1.368880, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 37576, "distinctRankCount": 1377, "maxRank": 20979.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 966284236, "mappedReadsCount": 584006115, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138853" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000909", "name": "CD8-positive, alpha-beta memory T cell" }, "cellTypeAuthorAnnotation": "CD8_TRM, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 29.772575, "sdRefIntergenicDistribution": 1.358661, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 34992, "distinctRankCount": 1347, "maxRank": 20985.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 966284236, "mappedReadsCount": 584006115, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138853" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000909", "name": "CD8-positive, alpha-beta memory T cell" }, "cellTypeAuthorAnnotation": "CD8_TRM/EM, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 21.515811, "sdRefIntergenicDistribution": 1.386496, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 49389, "distinctRankCount": 1501, "maxRank": 21524.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 966284236, "mappedReadsCount": 584006115, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138853" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000897", "name": "CD4-positive, alpha-beta memory T cell" }, "cellTypeAuthorAnnotation": "CD4_TRM, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 49.902099, "sdRefIntergenicDistribution": 1.284127, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 20465, "distinctRankCount": 905, "maxRank": 20081.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 966284236, "mappedReadsCount": 584006115, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138853" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000146", "name": "simple columnar epithelial cell" }, "cellTypeAuthorAnnotation": "SMG_Duct, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 89.817514, "sdRefIntergenicDistribution": 1.329126, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 11268, "distinctRankCount": 660, "maxRank": 19426.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 966284236, "mappedReadsCount": 584006115, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138853" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000097", "name": "mast cell" }, "cellTypeAuthorAnnotation": "Mast_cell , Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 22.402266, "sdRefIntergenicDistribution": 1.489441, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 48501, "distinctRankCount": 1572, "maxRank": 21351.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 966284236, "mappedReadsCount": 584006115, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138853" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002633", "name": "respiratory basal cell" }, "cellTypeAuthorAnnotation": "Basal, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 3.227929, "sdRefIntergenicDistribution": 1.922205, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 464087, "distinctRankCount": 3921, "maxRank": 25429.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 966284236, "mappedReadsCount": 584006115, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138853" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002633", "name": "respiratory basal cell" }, "cellTypeAuthorAnnotation": "Dividing_Basal, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 17.593316, "sdRefIntergenicDistribution": 1.476631, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 62902, "distinctRankCount": 2327, "maxRank": 21819.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 966284236, "mappedReadsCount": 584006115, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138853" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002633", "name": "respiratory basal cell" }, "cellTypeAuthorAnnotation": "SMG_Basal, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 204.073314, "sdRefIntergenicDistribution": 1.219233, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 4817, "distinctRankCount": 288, "maxRank": 18566.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 966284236, "mappedReadsCount": 584006115, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138853" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000624", "name": "CD4-positive, alpha-beta T cell" }, "cellTypeAuthorAnnotation": "CD4_EM/Effector, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 6.727906, "sdRefIntergenicDistribution": 1.596969, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 178195, "distinctRankCount": 2468, "maxRank": 24022.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 966284236, "mappedReadsCount": 584006115, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138853" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000624", "name": "CD4-positive, alpha-beta T cell" }, "cellTypeAuthorAnnotation": "CD4_naive/CM, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 14.126602, "sdRefIntergenicDistribution": 1.434094, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 76020, "distinctRankCount": 1843, "maxRank": 22344.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 966284236, "mappedReadsCount": 584006115, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138853" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000583", "name": "alveolar macrophage" }, "cellTypeAuthorAnnotation": "Macro_alveolar, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 4.021342, "sdRefIntergenicDistribution": 1.852988, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 350142, "distinctRankCount": 3581, "maxRank": 24495.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 966284236, "mappedReadsCount": 584006115, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138853" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000583", "name": "alveolar macrophage" }, "cellTypeAuthorAnnotation": "Macro_alveolar_metallothioneins, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 45.253509, "sdRefIntergenicDistribution": 1.336237, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 22475, "distinctRankCount": 980, "maxRank": 20020.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 966284236, "mappedReadsCount": 584006115, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138853" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000815", "name": "regulatory T cell" }, "cellTypeAuthorAnnotation": "T_reg, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 43.808621, "sdRefIntergenicDistribution": 1.297349, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 23324, "distinctRankCount": 982, "maxRank": 20326.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 966284236, "mappedReadsCount": 584006115, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138853" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002553", "name": "fibroblast of lung" }, "cellTypeAuthorAnnotation": "Fibro_adventitial, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 3.709996, "sdRefIntergenicDistribution": 1.854149, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 383094, "distinctRankCount": 3427, "maxRank": 24971.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 966284236, "mappedReadsCount": 584006115, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138853" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002553", "name": "fibroblast of lung" }, "cellTypeAuthorAnnotation": "Fibro_alveolar, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 2.876041, "sdRefIntergenicDistribution": 2.050672, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 572673, "distinctRankCount": 3824, "maxRank": 25718.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 966284236, "mappedReadsCount": 584006115, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138853" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002553", "name": "fibroblast of lung" }, "cellTypeAuthorAnnotation": "Fibro_peribronchial, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 10.519223, "sdRefIntergenicDistribution": 1.487084, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 104790, "distinctRankCount": 2316, "maxRank": 22709.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 966284236, "mappedReadsCount": 584006115, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138853" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002553", "name": "fibroblast of lung" }, "cellTypeAuthorAnnotation": "Fibro_perichondrial, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 39.397268, "sdRefIntergenicDistribution": 1.321689, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 25647, "distinctRankCount": 1171, "maxRank": 20601.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 966284236, "mappedReadsCount": 584006115, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138853" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:1001603", "name": "lung macrophage" }, "cellTypeAuthorAnnotation": "Macro_CCL, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 176.372898, "sdRefIntergenicDistribution": 1.267613, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 5682, "distinctRankCount": 442, "maxRank": 18567.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 966284236, "mappedReadsCount": 584006115, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138853" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:1001603", "name": "lung macrophage" }, "cellTypeAuthorAnnotation": "Macro_CHIT1, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 46.373801, "sdRefIntergenicDistribution": 1.318765, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 21987, "distinctRankCount": 1233, "maxRank": 20225.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 966284236, "mappedReadsCount": 584006115, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138853" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:1001603", "name": "lung macrophage" }, "cellTypeAuthorAnnotation": "Macro_intermediate, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 32.951825, "sdRefIntergenicDistribution": 1.357871, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 31266, "distinctRankCount": 1330, "maxRank": 20690.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 966284236, "mappedReadsCount": 584006115, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138853" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:1001603", "name": "lung macrophage" }, "cellTypeAuthorAnnotation": "Macro_interstitial, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 332.398598, "sdRefIntergenicDistribution": 1.237635, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 3065, "distinctRankCount": 144, "maxRank": 18259.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 966284236, "mappedReadsCount": 584006115, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138853" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:1001603", "name": "lung macrophage" }, "cellTypeAuthorAnnotation": "Macro_intravascular, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 48.067923, "sdRefIntergenicDistribution": 1.277346, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 20599, "distinctRankCount": 1078, "maxRank": 20086.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 966284236, "mappedReadsCount": 584006115, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138853" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000623", "name": "natural killer cell" }, "cellTypeAuthorAnnotation": "NK_CD11d, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 143.960725, "sdRefIntergenicDistribution": 1.288928, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 7129, "distinctRankCount": 338, "maxRank": 18905.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 966284236, "mappedReadsCount": 584006115, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138853" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000623", "name": "natural killer cell" }, "cellTypeAuthorAnnotation": "NK_CD16hi, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 8.188298, "sdRefIntergenicDistribution": 1.561125, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 142680, "distinctRankCount": 2258, "maxRank": 23508.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 966284236, "mappedReadsCount": 584006115, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138853" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000623", "name": "natural killer cell" }, "cellTypeAuthorAnnotation": "NK_CD56bright, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 223.841337, "sdRefIntergenicDistribution": 1.207141, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 4357, "distinctRankCount": 192, "maxRank": 18550.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 966284236, "mappedReadsCount": 584006115, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138853" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000985", "name": "IgG plasma cell" }, "cellTypeAuthorAnnotation": "B_plasma_IgG, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 97.202691, "sdRefIntergenicDistribution": 1.243230, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 9891, "distinctRankCount": 635, "maxRank": 19370.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 966284236, "mappedReadsCount": 584006115, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138853" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0009115", "name": "lymph node lymphatic vessel endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_Lymphatic, Vascular", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 6.580294, "sdRefIntergenicDistribution": 1.593603, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 179135, "distinctRankCount": 3032, "maxRank": 24170.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 966284236, "mappedReadsCount": 584006115, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138853" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000913", "name": "effector memory CD8-positive, alpha-beta T cell" }, "cellTypeAuthorAnnotation": "CD8_EM, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 30.375965, "sdRefIntergenicDistribution": 1.390916, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 35102, "distinctRankCount": 1225, "maxRank": 20873.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 966284236, "mappedReadsCount": 584006115, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138853" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000913", "name": "effector memory CD8-positive, alpha-beta T cell" }, "cellTypeAuthorAnnotation": "CD8_EM/EMRA, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 68.247931, "sdRefIntergenicDistribution": 1.333082, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 15340, "distinctRankCount": 709, "maxRank": 19831.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 966284236, "mappedReadsCount": 584006115, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138853" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000186", "name": "myofibroblast cell" }, "cellTypeAuthorAnnotation": "Fibro_myofibroblast, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 55.569643, "sdRefIntergenicDistribution": 1.362889, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 18975, "distinctRankCount": 1010, "maxRank": 20003.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 966284236, "mappedReadsCount": 584006115, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138853" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000158", "name": "club cell" }, "cellTypeAuthorAnnotation": "Secretory_Club, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 14.276777, "sdRefIntergenicDistribution": 1.486538, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 77896, "distinctRankCount": 2196, "maxRank": 22329.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 966284236, "mappedReadsCount": 584006115, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138853" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0001065", "name": "innate lymphoid cell" }, "cellTypeAuthorAnnotation": "ILC, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 1279.912643, "sdRefIntergenicDistribution": 1.159099, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 762, "distinctRankCount": 16, "maxRank": 17822.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 966284236, "mappedReadsCount": 584006115, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138853" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000192", "name": "smooth muscle cell" }, "cellTypeAuthorAnnotation": "Muscle_smooth_pulmonary, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 27.632655, "sdRefIntergenicDistribution": 1.312986, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 36422, "distinctRankCount": 1451, "maxRank": 21314.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 966284236, "mappedReadsCount": 584006115, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138853" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000990", "name": "conventional dendritic cell" }, "cellTypeAuthorAnnotation": "DC_1, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 248.426624, "sdRefIntergenicDistribution": 1.244883, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 3918, "distinctRankCount": 215, "maxRank": 18463.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 966284236, "mappedReadsCount": 584006115, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138853" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000990", "name": "conventional dendritic cell" }, "cellTypeAuthorAnnotation": "DC_2, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 116.854683, "sdRefIntergenicDistribution": 1.381330, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 8541, "distinctRankCount": 634, "maxRank": 19205.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 966284236, "mappedReadsCount": 584006115, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138853" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0019018", "name": "blood vessel smooth muscle cell" }, "cellTypeAuthorAnnotation": "Muscle_perivascular_immune_recruiting, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 50.361122, "sdRefIntergenicDistribution": 1.341544, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 20531, "distinctRankCount": 1099, "maxRank": 20066.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 966284236, "mappedReadsCount": 584006115, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138853" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0019018", "name": "blood vessel smooth muscle cell" }, "cellTypeAuthorAnnotation": "Muscle_smooth_arterial_systemic, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 66.941132, "sdRefIntergenicDistribution": 1.268901, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 15188, "distinctRankCount": 754, "maxRank": 19545.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 966284236, "mappedReadsCount": 584006115, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138853" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0001054", "name": "CD14-positive monocyte" }, "cellTypeAuthorAnnotation": "Monocyte_CD14, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 17.687243, "sdRefIntergenicDistribution": 1.397144, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 59908, "distinctRankCount": 1696, "maxRank": 21980.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 966284236, "mappedReadsCount": 584006115, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138853" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002063", "name": "type II pneumocyte" }, "cellTypeAuthorAnnotation": "AT2, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 0.897514, "sdRefIntergenicDistribution": 3.001865, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 5591221, "distinctRankCount": 7113, "maxRank": 27997.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 966284236, "mappedReadsCount": 584006115, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138853" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002063", "name": "type II pneumocyte" }, "cellTypeAuthorAnnotation": "Dividing_AT2, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 198.264453, "sdRefIntergenicDistribution": 1.151144, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 4834, "distinctRankCount": 315, "maxRank": 18557.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 966284236, "mappedReadsCount": 584006115, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138853" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002543", "name": "vein endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_venous_pulmonary, Vascular", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 46.872968, "sdRefIntergenicDistribution": 1.303636, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 21351, "distinctRankCount": 1106, "maxRank": 20294.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 966284236, "mappedReadsCount": 584006115, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138853" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002543", "name": "vein endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_venous_systemic, Vascular", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 23.938669, "sdRefIntergenicDistribution": 1.366752, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 43624, "distinctRankCount": 1485, "maxRank": 21408.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 966284236, "mappedReadsCount": 584006115, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138853" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0009089", "name": "lung pericyte" }, "cellTypeAuthorAnnotation": "Muscle_pericyte_pulmonary, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 65.260705, "sdRefIntergenicDistribution": 1.316204, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 15659, "distinctRankCount": 790, "maxRank": 19543.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 966284236, "mappedReadsCount": 584006115, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138853" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000814", "name": "mature NK T cell" }, "cellTypeAuthorAnnotation": "NKT, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 44.684939, "sdRefIntergenicDistribution": 1.315596, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 23082, "distinctRankCount": 931, "maxRank": 20459.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 966284236, "mappedReadsCount": 584006115, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138853" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000160", "name": "goblet cell" }, "cellTypeAuthorAnnotation": "Secretory_Goblet, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 12.108323, "sdRefIntergenicDistribution": 1.578815, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 96422, "distinctRankCount": 2462, "maxRank": 22140.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 966284236, "mappedReadsCount": 584006115, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138853" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000940", "name": "mucosal invariant T cell" }, "cellTypeAuthorAnnotation": "MAIT, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 93.211299, "sdRefIntergenicDistribution": 1.214513, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 10674, "distinctRankCount": 566, "maxRank": 19356.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 966284236, "mappedReadsCount": 584006115, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138853" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000319", "name": "mucus secreting cell" }, "cellTypeAuthorAnnotation": "SMG_Mucous, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 49.771137, "sdRefIntergenicDistribution": 1.374873, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 20638, "distinctRankCount": 1014, "maxRank": 20276.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 966284236, "mappedReadsCount": 584006115, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138853" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:1001568", "name": "pulmonary artery endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_arterial_pulmonary, Vascular", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 34.278443, "sdRefIntergenicDistribution": 1.344085, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 29733, "distinctRankCount": 1203, "maxRank": 20672.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 966284236, "mappedReadsCount": 584006115, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138853" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000185", "name": "myoepithelial cell" }, "cellTypeAuthorAnnotation": "Myoepithelial, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 405.713823, "sdRefIntergenicDistribution": 1.201962, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 2386, "distinctRankCount": 96, "maxRank": 18185.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 966284236, "mappedReadsCount": 584006115, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138853" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000798", "name": "gamma-delta T cell" }, "cellTypeAuthorAnnotation": "gdT, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 273.322016, "sdRefIntergenicDistribution": 1.144911, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 3456, "distinctRankCount": 207, "maxRank": 18372.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 966284236, "mappedReadsCount": 584006115, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138853" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000788", "name": "naive B cell" }, "cellTypeAuthorAnnotation": "B_naive, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 183.212487, "sdRefIntergenicDistribution": 1.290733, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 5448, "distinctRankCount": 313, "maxRank": 18732.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 966284236, "mappedReadsCount": 584006115, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138853" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000987", "name": "IgA plasma cell" }, "cellTypeAuthorAnnotation": "B_plasma_IgA, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 27.642449, "sdRefIntergenicDistribution": 1.471746, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 40415, "distinctRankCount": 1382, "maxRank": 20806.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 966284236, "mappedReadsCount": 584006115, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138853" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000057", "name": "fibroblast" }, "cellTypeAuthorAnnotation": "NAF_endoneurial, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 48.897022, "sdRefIntergenicDistribution": 1.373357, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 21771, "distinctRankCount": 1329, "maxRank": 20184.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 966284236, "mappedReadsCount": 584006115, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138853" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000057", "name": "fibroblast" }, "cellTypeAuthorAnnotation": "NAF_perineurial, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 65.114133, "sdRefIntergenicDistribution": 1.327126, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 15891, "distinctRankCount": 827, "maxRank": 19751.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 966284236, "mappedReadsCount": 584006115, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138853" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002376", "name": "non-myelinating Schwann cell" }, "cellTypeAuthorAnnotation": "Schwann_nonmyelinating, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 120.232326, "sdRefIntergenicDistribution": 1.220014, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 8398, "distinctRankCount": 448, "maxRank": 19147.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 966284236, "mappedReadsCount": 584006115, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138853" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000787", "name": "memory B cell" }, "cellTypeAuthorAnnotation": "B_memory, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 62.798154, "sdRefIntergenicDistribution": 1.356121, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 16268, "distinctRankCount": 833, "maxRank": 19860.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 966284236, "mappedReadsCount": 584006115, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138853" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000138", "name": "chondrocyte" }, "cellTypeAuthorAnnotation": "Chondrocyte, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 3.137782, "sdRefIntergenicDistribution": 1.973495, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 500837, "distinctRankCount": 4315, "maxRank": 25448.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 966284236, "mappedReadsCount": 584006115, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138853" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002368", "name": "respiratory epithelial cell" }, "cellTypeAuthorAnnotation": "Suprabasal, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 5.915178, "sdRefIntergenicDistribution": 1.701433, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 214158, "distinctRankCount": 3444, "maxRank": 24051.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 966284236, "mappedReadsCount": 584006115, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138853" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000165", "name": "neuroendocrine cell" }, "cellTypeAuthorAnnotation": "Neuroendocrine, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 759.686086, "sdRefIntergenicDistribution": 1.352235, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1356, "distinctRankCount": 36, "maxRank": 17903.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 966284236, "mappedReadsCount": 584006115, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138853" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:1000413", "name": "endothelial cell of artery" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_arterial_systemic, Vascular", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 128.298535, "sdRefIntergenicDistribution": 1.297985, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 8001, "distinctRankCount": 549, "maxRank": 18972.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 966284236, "mappedReadsCount": 584006115, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138853" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000784", "name": "plasmacytoid dendritic cell" }, "cellTypeAuthorAnnotation": "DC_plasmacytoid, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 1408.399678, "sdRefIntergenicDistribution": 1.161173, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 690, "distinctRankCount": 29, "maxRank": 17784.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 966284236, "mappedReadsCount": 584006115, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138853" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002062", "name": "type I pneumocyte" }, "cellTypeAuthorAnnotation": "AT1 , Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 1.879300, "sdRefIntergenicDistribution": 2.296103, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1078293, "distinctRankCount": 4944, "maxRank": 26292.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 966284236, "mappedReadsCount": 584006115, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138853" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000669", "name": "pericyte cell" }, "cellTypeAuthorAnnotation": "Muscle_pericyte_systemic, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 65.206784, "sdRefIntergenicDistribution": 1.287641, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 15274, "distinctRankCount": 693, "maxRank": 19489.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 966284236, "mappedReadsCount": 584006115, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138853" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000556", "name": "megakaryocyte" }, "cellTypeAuthorAnnotation": "Megakaryocyte, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 250.874911, "sdRefIntergenicDistribution": 1.214021, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 4011, "distinctRankCount": 185, "maxRank": 18120.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 859214933, "mappedReadsCount": 505659384, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138854" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002144", "name": "capillary endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_Cap_a, Vascular", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 6.772861, "sdRefIntergenicDistribution": 1.683724, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 183463, "distinctRankCount": 2555, "maxRank": 23789.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 859214933, "mappedReadsCount": 505659384, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138854" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002144", "name": "capillary endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_Cap_g, Vascular", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 4.000559, "sdRefIntergenicDistribution": 1.907228, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 365342, "distinctRankCount": 3272, "maxRank": 25020.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 859214933, "mappedReadsCount": 505659384, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138854" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000067", "name": "ciliated epithelial cell" }, "cellTypeAuthorAnnotation": "Ciliated, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 4.095025, "sdRefIntergenicDistribution": 2.115632, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 383701, "distinctRankCount": 4307, "maxRank": 24968.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 859214933, "mappedReadsCount": 505659384, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138854" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002396", "name": "CD14-low, CD16-positive monocyte" }, "cellTypeAuthorAnnotation": "Monocyte_CD16, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 6.986486, "sdRefIntergenicDistribution": 1.599960, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 171004, "distinctRankCount": 2735, "maxRank": 23516.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 859214933, "mappedReadsCount": 505659384, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138854" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000909", "name": "CD8-positive, alpha-beta memory T cell" }, "cellTypeAuthorAnnotation": "CD8_TRM, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 5.702786, "sdRefIntergenicDistribution": 1.670901, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 220852, "distinctRankCount": 2750, "maxRank": 23984.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 859214933, "mappedReadsCount": 505659384, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138854" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000909", "name": "CD8-positive, alpha-beta memory T cell" }, "cellTypeAuthorAnnotation": "CD8_TRM/EM, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 8.664132, "sdRefIntergenicDistribution": 1.581005, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 134591, "distinctRankCount": 2329, "maxRank": 23184.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 859214933, "mappedReadsCount": 505659384, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138854" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000897", "name": "CD4-positive, alpha-beta memory T cell" }, "cellTypeAuthorAnnotation": "CD4_TRM, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 30.086659, "sdRefIntergenicDistribution": 1.335651, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 34826, "distinctRankCount": 1218, "maxRank": 21042.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 859214933, "mappedReadsCount": 505659384, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138854" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000146", "name": "simple columnar epithelial cell" }, "cellTypeAuthorAnnotation": "SMG_Duct, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 11.174610, "sdRefIntergenicDistribution": 1.536829, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 103075, "distinctRankCount": 2391, "maxRank": 22644.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 859214933, "mappedReadsCount": 505659384, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138854" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000097", "name": "mast cell" }, "cellTypeAuthorAnnotation": "Mast_cell , Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 12.111141, "sdRefIntergenicDistribution": 1.566375, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 92943, "distinctRankCount": 2049, "maxRank": 22465.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 859214933, "mappedReadsCount": 505659384, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138854" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002633", "name": "respiratory basal cell" }, "cellTypeAuthorAnnotation": "Basal, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 7.214978, "sdRefIntergenicDistribution": 1.693163, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 173146, "distinctRankCount": 3019, "maxRank": 23826.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 859214933, "mappedReadsCount": 505659384, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138854" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002633", "name": "respiratory basal cell" }, "cellTypeAuthorAnnotation": "Dividing_Basal, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 160.835674, "sdRefIntergenicDistribution": 1.224700, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 5924, "distinctRankCount": 338, "maxRank": 18813.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 859214933, "mappedReadsCount": 505659384, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138854" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002633", "name": "respiratory basal cell" }, "cellTypeAuthorAnnotation": "SMG_Basal, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 62.571031, "sdRefIntergenicDistribution": 1.410815, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 17255, "distinctRankCount": 1094, "maxRank": 19641.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 859214933, "mappedReadsCount": 505659384, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138854" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000624", "name": "CD4-positive, alpha-beta T cell" }, "cellTypeAuthorAnnotation": "CD4_EM/Effector, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 5.087484, "sdRefIntergenicDistribution": 1.699523, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 252507, "distinctRankCount": 2662, "maxRank": 24333.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 859214933, "mappedReadsCount": 505659384, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138854" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000624", "name": "CD4-positive, alpha-beta T cell" }, "cellTypeAuthorAnnotation": "CD4_naive/CM, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 3.967106, "sdRefIntergenicDistribution": 1.781693, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 342386, "distinctRankCount": 3243, "maxRank": 24905.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 859214933, "mappedReadsCount": 505659384, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138854" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000583", "name": "alveolar macrophage" }, "cellTypeAuthorAnnotation": "Macro_alveolar, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 4.964631, "sdRefIntergenicDistribution": 1.792097, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 267192, "distinctRankCount": 3329, "maxRank": 24370.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 859214933, "mappedReadsCount": 505659384, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138854" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000583", "name": "alveolar macrophage" }, "cellTypeAuthorAnnotation": "Macro_alveolar_metallothioneins, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 302.166180, "sdRefIntergenicDistribution": 1.176235, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 3199, "distinctRankCount": 121, "maxRank": 18321.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 859214933, "mappedReadsCount": 505659384, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138854" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000815", "name": "regulatory T cell" }, "cellTypeAuthorAnnotation": "T_reg, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 21.936446, "sdRefIntergenicDistribution": 1.417813, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 49270, "distinctRankCount": 1503, "maxRank": 21473.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 859214933, "mappedReadsCount": 505659384, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138854" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002553", "name": "fibroblast of lung" }, "cellTypeAuthorAnnotation": "Fibro_adventitial, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 2.319071, "sdRefIntergenicDistribution": 2.022389, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 740144, "distinctRankCount": 4465, "maxRank": 26219.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 859214933, "mappedReadsCount": 505659384, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138854" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002553", "name": "fibroblast of lung" }, "cellTypeAuthorAnnotation": "Fibro_alveolar, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 1.667944, "sdRefIntergenicDistribution": 2.330507, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1362709, "distinctRankCount": 5076, "maxRank": 26951.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 859214933, "mappedReadsCount": 505659384, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138854" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002553", "name": "fibroblast of lung" }, "cellTypeAuthorAnnotation": "Fibro_peribronchial, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 6.604900, "sdRefIntergenicDistribution": 1.627791, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 184437, "distinctRankCount": 3051, "maxRank": 23925.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 859214933, "mappedReadsCount": 505659384, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138854" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002553", "name": "fibroblast of lung" }, "cellTypeAuthorAnnotation": "Fibro_perichondrial, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 26.096093, "sdRefIntergenicDistribution": 1.425487, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 41259, "distinctRankCount": 1565, "maxRank": 21025.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 859214933, "mappedReadsCount": 505659384, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138854" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:1001603", "name": "lung macrophage" }, "cellTypeAuthorAnnotation": "Macro_CCL, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 174.029918, "sdRefIntergenicDistribution": 1.323145, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 5754, "distinctRankCount": 235, "maxRank": 18622.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 859214933, "mappedReadsCount": 505659384, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138854" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:1001603", "name": "lung macrophage" }, "cellTypeAuthorAnnotation": "Macro_CHIT1, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 52.744424, "sdRefIntergenicDistribution": 1.334962, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 19718, "distinctRankCount": 982, "maxRank": 19977.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 859214933, "mappedReadsCount": 505659384, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138854" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:1001603", "name": "lung macrophage" }, "cellTypeAuthorAnnotation": "Macro_dividing, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 136.083536, "sdRefIntergenicDistribution": 1.376228, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 7526, "distinctRankCount": 517, "maxRank": 18856.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 859214933, "mappedReadsCount": 505659384, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138854" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:1001603", "name": "lung macrophage" }, "cellTypeAuthorAnnotation": "Macro_intermediate, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 20.646806, "sdRefIntergenicDistribution": 1.416087, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 52854, "distinctRankCount": 1733, "maxRank": 21116.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 859214933, "mappedReadsCount": 505659384, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138854" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:1001603", "name": "lung macrophage" }, "cellTypeAuthorAnnotation": "Macro_interstitial, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 147.237374, "sdRefIntergenicDistribution": 1.277267, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 6627, "distinctRankCount": 350, "maxRank": 18848.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 859214933, "mappedReadsCount": 505659384, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138854" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:1001603", "name": "lung macrophage" }, "cellTypeAuthorAnnotation": "Macro_intravascular, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 14.224734, "sdRefIntergenicDistribution": 1.484438, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 77318, "distinctRankCount": 2107, "maxRank": 22102.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 859214933, "mappedReadsCount": 505659384, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138854" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000623", "name": "natural killer cell" }, "cellTypeAuthorAnnotation": "NK_CD11d, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 18.790137, "sdRefIntergenicDistribution": 1.509316, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 58832, "distinctRankCount": 1606, "maxRank": 21853.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 859214933, "mappedReadsCount": 505659384, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138854" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000623", "name": "natural killer cell" }, "cellTypeAuthorAnnotation": "NK_CD16hi, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 4.267759, "sdRefIntergenicDistribution": 1.794350, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 316351, "distinctRankCount": 2978, "maxRank": 24892.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 859214933, "mappedReadsCount": 505659384, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138854" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000623", "name": "natural killer cell" }, "cellTypeAuthorAnnotation": "NK_CD56bright, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 99.461478, "sdRefIntergenicDistribution": 1.308222, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 10471, "distinctRankCount": 511, "maxRank": 19343.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 859214933, "mappedReadsCount": 505659384, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138854" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000985", "name": "IgG plasma cell" }, "cellTypeAuthorAnnotation": "B_plasma_IgG, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 20.292788, "sdRefIntergenicDistribution": 1.534075, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 55114, "distinctRankCount": 1820, "maxRank": 21509.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 859214933, "mappedReadsCount": 505659384, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138854" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0009115", "name": "lymph node lymphatic vessel endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_Lymphatic, Vascular", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 5.506240, "sdRefIntergenicDistribution": 1.663919, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 228497, "distinctRankCount": 3430, "maxRank": 24251.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 859214933, "mappedReadsCount": 505659384, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138854" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000913", "name": "effector memory CD8-positive, alpha-beta T cell" }, "cellTypeAuthorAnnotation": "CD8_EM, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 11.175330, "sdRefIntergenicDistribution": 1.498191, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 102252, "distinctRankCount": 2008, "maxRank": 22557.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 859214933, "mappedReadsCount": 505659384, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138854" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000913", "name": "effector memory CD8-positive, alpha-beta T cell" }, "cellTypeAuthorAnnotation": "CD8_EM/EMRA, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 12.565732, "sdRefIntergenicDistribution": 1.492924, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 88419, "distinctRankCount": 2015, "maxRank": 22419.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 859214933, "mappedReadsCount": 505659384, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138854" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000186", "name": "myofibroblast cell" }, "cellTypeAuthorAnnotation": "Fibro_myofibroblast, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 23.478140, "sdRefIntergenicDistribution": 1.414118, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 45260, "distinctRankCount": 1634, "maxRank": 21506.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 859214933, "mappedReadsCount": 505659384, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138854" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000158", "name": "club cell" }, "cellTypeAuthorAnnotation": "Secretory_Club, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 3.374777, "sdRefIntergenicDistribution": 1.851230, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 428839, "distinctRankCount": 3751, "maxRank": 24830.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 859214933, "mappedReadsCount": 505659384, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138854" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0001065", "name": "innate lymphoid cell" }, "cellTypeAuthorAnnotation": "ILC, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 164.530509, "sdRefIntergenicDistribution": 1.235199, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 5987, "distinctRankCount": 283, "maxRank": 18814.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 859214933, "mappedReadsCount": 505659384, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138854" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000192", "name": "smooth muscle cell" }, "cellTypeAuthorAnnotation": "Muscle_smooth_pulmonary, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 10.358546, "sdRefIntergenicDistribution": 1.451809, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 107926, "distinctRankCount": 2453, "maxRank": 22812.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 859214933, "mappedReadsCount": 505659384, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138854" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0019001", "name": "tracheobronchial serous cell" }, "cellTypeAuthorAnnotation": "SMG_Serous, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 1.249304, "sdRefIntergenicDistribution": 2.529531, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 2153683, "distinctRankCount": 6042, "maxRank": 27025.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 859214933, "mappedReadsCount": 505659384, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138854" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0019019", "name": "tracheobronchial smooth muscle cell" }, "cellTypeAuthorAnnotation": "Muscle_smooth_airway, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 12.484247, "sdRefIntergenicDistribution": 1.469984, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 90995, "distinctRankCount": 2134, "maxRank": 21788.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 859214933, "mappedReadsCount": 505659384, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138854" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000990", "name": "conventional dendritic cell" }, "cellTypeAuthorAnnotation": "DC_1, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 40.124324, "sdRefIntergenicDistribution": 1.392903, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 26145, "distinctRankCount": 1207, "maxRank": 20112.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 859214933, "mappedReadsCount": 505659384, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138854" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000990", "name": "conventional dendritic cell" }, "cellTypeAuthorAnnotation": "DC_2, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 37.228118, "sdRefIntergenicDistribution": 1.381136, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 28229, "distinctRankCount": 1414, "maxRank": 20538.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 859214933, "mappedReadsCount": 505659384, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138854" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000990", "name": "conventional dendritic cell" }, "cellTypeAuthorAnnotation": "DC_activated, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 145.008169, "sdRefIntergenicDistribution": 1.225486, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 6769, "distinctRankCount": 405, "maxRank": 18832.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 859214933, "mappedReadsCount": 505659384, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138854" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0019018", "name": "blood vessel smooth muscle cell" }, "cellTypeAuthorAnnotation": "Muscle_perivascular_immune_recruiting, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 54.381737, "sdRefIntergenicDistribution": 1.314987, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 18927, "distinctRankCount": 868, "maxRank": 19804.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 859214933, "mappedReadsCount": 505659384, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138854" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0019018", "name": "blood vessel smooth muscle cell" }, "cellTypeAuthorAnnotation": "Muscle_smooth_arterial_systemic, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 34.109702, "sdRefIntergenicDistribution": 1.367145, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 31471, "distinctRankCount": 1185, "maxRank": 20486.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 859214933, "mappedReadsCount": 505659384, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138854" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0001054", "name": "CD14-positive monocyte" }, "cellTypeAuthorAnnotation": "Monocyte_CD14, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 10.281098, "sdRefIntergenicDistribution": 1.486055, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 109031, "distinctRankCount": 2427, "maxRank": 22789.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 859214933, "mappedReadsCount": 505659384, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138854" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002063", "name": "type II pneumocyte" }, "cellTypeAuthorAnnotation": "AT2, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 0.909763, "sdRefIntergenicDistribution": 2.959128, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 5254755, "distinctRankCount": 7003, "maxRank": 27823.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 859214933, "mappedReadsCount": 505659384, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138854" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002063", "name": "type II pneumocyte" }, "cellTypeAuthorAnnotation": "Dividing_AT2, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 221.307160, "sdRefIntergenicDistribution": 1.300621, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 4536, "distinctRankCount": 317, "maxRank": 18498.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 859214933, "mappedReadsCount": 505659384, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138854" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002543", "name": "vein endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_venous_pulmonary, Vascular", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 10.825002, "sdRefIntergenicDistribution": 1.545187, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 106012, "distinctRankCount": 2460, "maxRank": 22591.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 859214933, "mappedReadsCount": 505659384, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138854" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002543", "name": "vein endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_venous_systemic, Vascular", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 8.596031, "sdRefIntergenicDistribution": 1.611994, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 139035, "distinctRankCount": 2544, "maxRank": 23337.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 859214933, "mappedReadsCount": 505659384, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138854" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0009089", "name": "lung pericyte" }, "cellTypeAuthorAnnotation": "Muscle_pericyte_pulmonary, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 19.259702, "sdRefIntergenicDistribution": 1.409959, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 56467, "distinctRankCount": 1719, "maxRank": 21408.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 859214933, "mappedReadsCount": 505659384, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138854" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000814", "name": "mature NK T cell" }, "cellTypeAuthorAnnotation": "NKT, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 16.183230, "sdRefIntergenicDistribution": 1.463084, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 68380, "distinctRankCount": 1686, "maxRank": 22050.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 859214933, "mappedReadsCount": 505659384, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138854" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000160", "name": "goblet cell" }, "cellTypeAuthorAnnotation": "Secretory_Goblet, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 2.455319, "sdRefIntergenicDistribution": 2.084907, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 695403, "distinctRankCount": 4795, "maxRank": 25681.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 859214933, "mappedReadsCount": 505659384, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138854" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000940", "name": "mucosal invariant T cell" }, "cellTypeAuthorAnnotation": "MAIT, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 20.333114, "sdRefIntergenicDistribution": 1.431471, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 52734, "distinctRankCount": 1492, "maxRank": 21561.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 859214933, "mappedReadsCount": 505659384, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138854" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000319", "name": "mucus secreting cell" }, "cellTypeAuthorAnnotation": "SMG_Mucous, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 0.919654, "sdRefIntergenicDistribution": 2.905542, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 4948525, "distinctRankCount": 7349, "maxRank": 27936.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 859214933, "mappedReadsCount": 505659384, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138854" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:1001568", "name": "pulmonary artery endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_arterial_pulmonary, Vascular", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 10.310721, "sdRefIntergenicDistribution": 1.556025, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 111940, "distinctRankCount": 2355, "maxRank": 22833.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 859214933, "mappedReadsCount": 505659384, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138854" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000185", "name": "myoepithelial cell" }, "cellTypeAuthorAnnotation": "Myoepithelial, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 18.955859, "sdRefIntergenicDistribution": 1.461874, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 57973, "distinctRankCount": 1884, "maxRank": 21519.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 859214933, "mappedReadsCount": 505659384, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138854" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000798", "name": "gamma-delta T cell" }, "cellTypeAuthorAnnotation": "gdT, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 59.796926, "sdRefIntergenicDistribution": 1.313051, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 17238, "distinctRankCount": 852, "maxRank": 19864.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 859214933, "mappedReadsCount": 505659384, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138854" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000788", "name": "naive B cell" }, "cellTypeAuthorAnnotation": "B_naive, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 26.871009, "sdRefIntergenicDistribution": 1.438587, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 39609, "distinctRankCount": 1348, "maxRank": 21018.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 859214933, "mappedReadsCount": 505659384, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138854" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000235", "name": "macrophage" }, "cellTypeAuthorAnnotation": "Macro_AW_CX3CR1, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 42.184993, "sdRefIntergenicDistribution": 1.255413, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 23719, "distinctRankCount": 1272, "maxRank": 20327.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 859214933, "mappedReadsCount": 505659384, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138854" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000987", "name": "IgA plasma cell" }, "cellTypeAuthorAnnotation": "B_plasma_IgA, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 7.919910, "sdRefIntergenicDistribution": 1.736638, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 156453, "distinctRankCount": 2563, "maxRank": 23073.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 859214933, "mappedReadsCount": 505659384, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138854" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000057", "name": "fibroblast" }, "cellTypeAuthorAnnotation": "NAF_endoneurial, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 97.178793, "sdRefIntergenicDistribution": 1.290741, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 10470, "distinctRankCount": 532, "maxRank": 19100.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 859214933, "mappedReadsCount": 505659384, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138854" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000057", "name": "fibroblast" }, "cellTypeAuthorAnnotation": "NAF_perineurial, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 46.067369, "sdRefIntergenicDistribution": 1.391503, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 22900, "distinctRankCount": 1153, "maxRank": 20266.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 859214933, "mappedReadsCount": 505659384, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138854" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002376", "name": "non-myelinating Schwann cell" }, "cellTypeAuthorAnnotation": "Schwann_nonmyelinating, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 76.407749, "sdRefIntergenicDistribution": 1.324286, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 13494, "distinctRankCount": 758, "maxRank": 19436.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 859214933, "mappedReadsCount": 505659384, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138854" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000787", "name": "memory B cell" }, "cellTypeAuthorAnnotation": "B_memory, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 22.418890, "sdRefIntergenicDistribution": 1.475129, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 48584, "distinctRankCount": 1566, "maxRank": 21320.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 859214933, "mappedReadsCount": 505659384, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138854" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000138", "name": "chondrocyte" }, "cellTypeAuthorAnnotation": "Chondrocyte, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 15.050524, "sdRefIntergenicDistribution": 1.537745, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 75409, "distinctRankCount": 2328, "maxRank": 21923.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 859214933, "mappedReadsCount": 505659384, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138854" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002368", "name": "respiratory epithelial cell" }, "cellTypeAuthorAnnotation": "Suprabasal, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 10.140697, "sdRefIntergenicDistribution": 1.598923, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 115986, "distinctRankCount": 2870, "maxRank": 23149.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 859214933, "mappedReadsCount": 505659384, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138854" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000165", "name": "neuroendocrine cell" }, "cellTypeAuthorAnnotation": "Neuroendocrine, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 158.246515, "sdRefIntergenicDistribution": 1.298576, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 6403, "distinctRankCount": 419, "maxRank": 18723.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 859214933, "mappedReadsCount": 505659384, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138854" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000077", "name": "mesothelial cell" }, "cellTypeAuthorAnnotation": "Mesothelia, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 60.751971, "sdRefIntergenicDistribution": 1.370813, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 17222, "distinctRankCount": 943, "maxRank": 19701.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 859214933, "mappedReadsCount": 505659384, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138854" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:1000413", "name": "endothelial cell of artery" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_arterial_systemic, Vascular", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 1434.678141, "sdRefIntergenicDistribution": 1.003212, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 662, "distinctRankCount": 36, "maxRank": 17781.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 859214933, "mappedReadsCount": 505659384, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138854" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000784", "name": "plasmacytoid dendritic cell" }, "cellTypeAuthorAnnotation": "DC_plasmacytoid, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 607.449338, "sdRefIntergenicDistribution": 1.263220, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1715, "distinctRankCount": 54, "maxRank": 18091.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 859214933, "mappedReadsCount": 505659384, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138854" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002062", "name": "type I pneumocyte" }, "cellTypeAuthorAnnotation": "AT1 , Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 1.560898, "sdRefIntergenicDistribution": 2.467122, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1542803, "distinctRankCount": 5536, "maxRank": 26739.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 859214933, "mappedReadsCount": 505659384, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138854" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:4033044", "name": "deuterosomal cell" }, "cellTypeAuthorAnnotation": "Deuterosomal, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 97.964032, "sdRefIntergenicDistribution": 1.420970, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 10871, "distinctRankCount": 787, "maxRank": 19168.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 859214933, "mappedReadsCount": 505659384, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138854" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000669", "name": "pericyte cell" }, "cellTypeAuthorAnnotation": "Muscle_pericyte_systemic, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 72.572975, "sdRefIntergenicDistribution": 1.274388, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 13726, "distinctRankCount": 761, "maxRank": 19161.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 775907445, "mappedReadsCount": 457089602, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138860" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002144", "name": "capillary endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_Cap_a, Vascular", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 42.816805, "sdRefIntergenicDistribution": 1.333166, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 24235, "distinctRankCount": 1178, "maxRank": 20517.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 775907445, "mappedReadsCount": 457089602, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138860" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002144", "name": "capillary endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_Cap_g, Vascular", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 20.880821, "sdRefIntergenicDistribution": 1.401681, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 50701, "distinctRankCount": 1705, "maxRank": 21908.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 775907445, "mappedReadsCount": 457089602, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138860" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000067", "name": "ciliated epithelial cell" }, "cellTypeAuthorAnnotation": "Ciliated, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 2.082421, "sdRefIntergenicDistribution": 2.574616, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1085518, "distinctRankCount": 5477, "maxRank": 26569.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 775907445, "mappedReadsCount": 457089602, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138860" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002396", "name": "CD14-low, CD16-positive monocyte" }, "cellTypeAuthorAnnotation": "Monocyte_CD16, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 14.618015, "sdRefIntergenicDistribution": 1.427717, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 73213, "distinctRankCount": 1898, "maxRank": 22273.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 775907445, "mappedReadsCount": 457089602, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138860" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000909", "name": "CD8-positive, alpha-beta memory T cell" }, "cellTypeAuthorAnnotation": "CD8_TRM, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 5.434021, "sdRefIntergenicDistribution": 1.706946, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 232963, "distinctRankCount": 2887, "maxRank": 24253.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 775907445, "mappedReadsCount": 457089602, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138860" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000909", "name": "CD8-positive, alpha-beta memory T cell" }, "cellTypeAuthorAnnotation": "CD8_TRM/EM, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 13.620970, "sdRefIntergenicDistribution": 1.530933, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 82422, "distinctRankCount": 1893, "maxRank": 22268.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 775907445, "mappedReadsCount": 457089602, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138860" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000897", "name": "CD4-positive, alpha-beta memory T cell" }, "cellTypeAuthorAnnotation": "CD4_TRM, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 18.614996, "sdRefIntergenicDistribution": 1.501246, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 59563, "distinctRankCount": 1652, "maxRank": 21866.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 775907445, "mappedReadsCount": 457089602, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138860" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000146", "name": "simple columnar epithelial cell" }, "cellTypeAuthorAnnotation": "SMG_Duct, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 8.637671, "sdRefIntergenicDistribution": 1.571614, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 136708, "distinctRankCount": 2804, "maxRank": 23318.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 775907445, "mappedReadsCount": 457089602, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138860" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000097", "name": "mast cell" }, "cellTypeAuthorAnnotation": "Mast_cell , Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 11.503586, "sdRefIntergenicDistribution": 1.583600, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 98681, "distinctRankCount": 2085, "maxRank": 22871.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 775907445, "mappedReadsCount": 457089602, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138860" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002633", "name": "respiratory basal cell" }, "cellTypeAuthorAnnotation": "Basal, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 5.290922, "sdRefIntergenicDistribution": 1.763118, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 248772, "distinctRankCount": 3430, "maxRank": 24514.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 775907445, "mappedReadsCount": 457089602, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138860" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002633", "name": "respiratory basal cell" }, "cellTypeAuthorAnnotation": "Dividing_Basal, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 35.562069, "sdRefIntergenicDistribution": 1.349701, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 29197, "distinctRankCount": 1688, "maxRank": 20731.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 775907445, "mappedReadsCount": 457089602, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138860" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002633", "name": "respiratory basal cell" }, "cellTypeAuthorAnnotation": "SMG_Basal, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 319.049814, "sdRefIntergenicDistribution": 1.259960, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 3190, "distinctRankCount": 263, "maxRank": 18196.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 775907445, "mappedReadsCount": 457089602, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138860" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000624", "name": "CD4-positive, alpha-beta T cell" }, "cellTypeAuthorAnnotation": "CD4_EM/Effector, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 4.617243, "sdRefIntergenicDistribution": 1.752233, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 284748, "distinctRankCount": 2858, "maxRank": 24890.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 775907445, "mappedReadsCount": 457089602, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138860" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000624", "name": "CD4-positive, alpha-beta T cell" }, "cellTypeAuthorAnnotation": "CD4_naive/CM, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 6.719075, "sdRefIntergenicDistribution": 1.622840, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 178830, "distinctRankCount": 2656, "maxRank": 24128.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 775907445, "mappedReadsCount": 457089602, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138860" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000583", "name": "alveolar macrophage" }, "cellTypeAuthorAnnotation": "Macro_alveolar, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 5.051349, "sdRefIntergenicDistribution": 1.705744, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 246790, "distinctRankCount": 3142, "maxRank": 24367.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 775907445, "mappedReadsCount": 457089602, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138860" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000583", "name": "alveolar macrophage" }, "cellTypeAuthorAnnotation": "Macro_alveolar_metallothioneins, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 519.307988, "sdRefIntergenicDistribution": 1.110094, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1810, "distinctRankCount": 66, "maxRank": 18027.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 775907445, "mappedReadsCount": 457089602, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138860" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000815", "name": "regulatory T cell" }, "cellTypeAuthorAnnotation": "T_reg, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 24.298514, "sdRefIntergenicDistribution": 1.392663, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 43562, "distinctRankCount": 1498, "maxRank": 21536.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 775907445, "mappedReadsCount": 457089602, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138860" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002553", "name": "fibroblast of lung" }, "cellTypeAuthorAnnotation": "Fibro_adventitial, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 1.743251, "sdRefIntergenicDistribution": 2.183078, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1156942, "distinctRankCount": 4819, "maxRank": 26954.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 775907445, "mappedReadsCount": 457089602, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138860" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002553", "name": "fibroblast of lung" }, "cellTypeAuthorAnnotation": "Fibro_alveolar, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 2.416766, "sdRefIntergenicDistribution": 2.008954, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 684095, "distinctRankCount": 4105, "maxRank": 26256.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 775907445, "mappedReadsCount": 457089602, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138860" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002553", "name": "fibroblast of lung" }, "cellTypeAuthorAnnotation": "Fibro_peribronchial, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 7.546219, "sdRefIntergenicDistribution": 1.584460, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 157851, "distinctRankCount": 2864, "maxRank": 23613.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 775907445, "mappedReadsCount": 457089602, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138860" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002553", "name": "fibroblast of lung" }, "cellTypeAuthorAnnotation": "Fibro_perichondrial, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 13.968731, "sdRefIntergenicDistribution": 1.454735, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 78641, "distinctRankCount": 2142, "maxRank": 22189.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 775907445, "mappedReadsCount": 457089602, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138860" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:1001603", "name": "lung macrophage" }, "cellTypeAuthorAnnotation": "Macro_CCL, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 383.610969, "sdRefIntergenicDistribution": 1.161026, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 2539, "distinctRankCount": 152, "maxRank": 18092.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 775907445, "mappedReadsCount": 457089602, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138860" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:1001603", "name": "lung macrophage" }, "cellTypeAuthorAnnotation": "Macro_CHIT1, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 5.673079, "sdRefIntergenicDistribution": 1.632623, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 213226, "distinctRankCount": 3113, "maxRank": 24346.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 775907445, "mappedReadsCount": 457089602, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138860" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:1001603", "name": "lung macrophage" }, "cellTypeAuthorAnnotation": "Macro_dividing, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 1796.553102, "sdRefIntergenicDistribution": 1.267130, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 561, "distinctRankCount": 22, "maxRank": 17762.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 775907445, "mappedReadsCount": 457089602, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138860" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:1001603", "name": "lung macrophage" }, "cellTypeAuthorAnnotation": "Macro_intermediate, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 31.851531, "sdRefIntergenicDistribution": 1.345800, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 32594, "distinctRankCount": 1569, "maxRank": 20912.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 775907445, "mappedReadsCount": 457089602, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138860" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:1001603", "name": "lung macrophage" }, "cellTypeAuthorAnnotation": "Macro_interstitial, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 138.443897, "sdRefIntergenicDistribution": 1.236880, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 7000, "distinctRankCount": 371, "maxRank": 18936.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 775907445, "mappedReadsCount": 457089602, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138860" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:1001603", "name": "lung macrophage" }, "cellTypeAuthorAnnotation": "Macro_intravascular, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 10.518540, "sdRefIntergenicDistribution": 1.529563, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 107508, "distinctRankCount": 2481, "maxRank": 22962.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 775907445, "mappedReadsCount": 457089602, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138860" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000623", "name": "natural killer cell" }, "cellTypeAuthorAnnotation": "NK_CD11d, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 56.415780, "sdRefIntergenicDistribution": 1.333368, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 18026, "distinctRankCount": 804, "maxRank": 20242.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 775907445, "mappedReadsCount": 457089602, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138860" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000623", "name": "natural killer cell" }, "cellTypeAuthorAnnotation": "NK_CD16hi, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 12.595138, "sdRefIntergenicDistribution": 1.508056, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 89015, "distinctRankCount": 1923, "maxRank": 22945.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 775907445, "mappedReadsCount": 457089602, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138860" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000623", "name": "natural killer cell" }, "cellTypeAuthorAnnotation": "NK_CD56bright, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 143.747972, "sdRefIntergenicDistribution": 1.202231, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 6714, "distinctRankCount": 375, "maxRank": 18987.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 775907445, "mappedReadsCount": 457089602, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138860" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000985", "name": "IgG plasma cell" }, "cellTypeAuthorAnnotation": "B_plasma_IgG, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 9.306852, "sdRefIntergenicDistribution": 1.659287, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 126747, "distinctRankCount": 2496, "maxRank": 23186.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 775907445, "mappedReadsCount": 457089602, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138860" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0009115", "name": "lymph node lymphatic vessel endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_Lymphatic, Vascular", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 6.516737, "sdRefIntergenicDistribution": 1.633558, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 186638, "distinctRankCount": 3140, "maxRank": 24194.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 775907445, "mappedReadsCount": 457089602, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138860" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000913", "name": "effector memory CD8-positive, alpha-beta T cell" }, "cellTypeAuthorAnnotation": "CD8_EM, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 13.415649, "sdRefIntergenicDistribution": 1.463552, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 81375, "distinctRankCount": 1842, "maxRank": 22468.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 775907445, "mappedReadsCount": 457089602, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138860" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000913", "name": "effector memory CD8-positive, alpha-beta T cell" }, "cellTypeAuthorAnnotation": "CD8_EM/EMRA, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 204.950859, "sdRefIntergenicDistribution": 1.168533, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 4748, "distinctRankCount": 312, "maxRank": 18563.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 775907445, "mappedReadsCount": 457089602, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138860" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000186", "name": "myofibroblast cell" }, "cellTypeAuthorAnnotation": "Fibro_myofibroblast, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 27.612027, "sdRefIntergenicDistribution": 1.399914, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 38169, "distinctRankCount": 1535, "maxRank": 21161.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 775907445, "mappedReadsCount": 457089602, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138860" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000158", "name": "club cell" }, "cellTypeAuthorAnnotation": "Secretory_Club, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 4.056021, "sdRefIntergenicDistribution": 1.735579, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 322447, "distinctRankCount": 3542, "maxRank": 24874.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 775907445, "mappedReadsCount": 457089602, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138860" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0001065", "name": "innate lymphoid cell" }, "cellTypeAuthorAnnotation": "ILC, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 87.060719, "sdRefIntergenicDistribution": 1.238896, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 11307, "distinctRankCount": 652, "maxRank": 19448.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 775907445, "mappedReadsCount": 457089602, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138860" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000192", "name": "smooth muscle cell" }, "cellTypeAuthorAnnotation": "Muscle_smooth_pulmonary, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 10.651306, "sdRefIntergenicDistribution": 1.463822, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 104776, "distinctRankCount": 2402, "maxRank": 22763.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 775907445, "mappedReadsCount": 457089602, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138860" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0019001", "name": "tracheobronchial serous cell" }, "cellTypeAuthorAnnotation": "SMG_Serous, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 1.643714, "sdRefIntergenicDistribution": 2.164431, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1159174, "distinctRankCount": 4875, "maxRank": 26381.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 775907445, "mappedReadsCount": 457089602, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138860" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0019019", "name": "tracheobronchial smooth muscle cell" }, "cellTypeAuthorAnnotation": "Muscle_smooth_airway, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 4.827967, "sdRefIntergenicDistribution": 1.706422, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 267132, "distinctRankCount": 3052, "maxRank": 24059.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 775907445, "mappedReadsCount": 457089602, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138860" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000990", "name": "conventional dendritic cell" }, "cellTypeAuthorAnnotation": "DC_1, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 31.101590, "sdRefIntergenicDistribution": 1.369616, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 33313, "distinctRankCount": 1443, "maxRank": 20712.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 775907445, "mappedReadsCount": 457089602, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138860" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000990", "name": "conventional dendritic cell" }, "cellTypeAuthorAnnotation": "DC_2, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 15.281658, "sdRefIntergenicDistribution": 1.432219, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 70683, "distinctRankCount": 1900, "maxRank": 22210.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 775907445, "mappedReadsCount": 457089602, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138860" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000990", "name": "conventional dendritic cell" }, "cellTypeAuthorAnnotation": "DC_activated, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 118.535108, "sdRefIntergenicDistribution": 1.339787, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 8192, "distinctRankCount": 441, "maxRank": 19009.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 775907445, "mappedReadsCount": 457089602, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138860" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0019018", "name": "blood vessel smooth muscle cell" }, "cellTypeAuthorAnnotation": "Muscle_perivascular_immune_recruiting, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 13.889460, "sdRefIntergenicDistribution": 1.427071, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 79411, "distinctRankCount": 1877, "maxRank": 21871.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 775907445, "mappedReadsCount": 457089602, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138860" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0019018", "name": "blood vessel smooth muscle cell" }, "cellTypeAuthorAnnotation": "Muscle_smooth_arterial_systemic, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 21.795390, "sdRefIntergenicDistribution": 1.389278, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 49334, "distinctRankCount": 1620, "maxRank": 21159.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 775907445, "mappedReadsCount": 457089602, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138860" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0001054", "name": "CD14-positive monocyte" }, "cellTypeAuthorAnnotation": "Monocyte_CD14, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 14.613062, "sdRefIntergenicDistribution": 1.413676, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 73519, "distinctRankCount": 1950, "maxRank": 22394.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 775907445, "mappedReadsCount": 457089602, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138860" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002063", "name": "type II pneumocyte" }, "cellTypeAuthorAnnotation": "AT2, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 0.890664, "sdRefIntergenicDistribution": 2.844884, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 4611321, "distinctRankCount": 6709, "maxRank": 27828.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 775907445, "mappedReadsCount": 457089602, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138860" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002063", "name": "type II pneumocyte" }, "cellTypeAuthorAnnotation": "Dividing_AT2, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 8.478738, "sdRefIntergenicDistribution": 1.524443, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 128809, "distinctRankCount": 2760, "maxRank": 23409.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 775907445, "mappedReadsCount": 457089602, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138860" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002543", "name": "vein endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_venous_pulmonary, Vascular", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 39.350938, "sdRefIntergenicDistribution": 1.367831, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 26513, "distinctRankCount": 1451, "maxRank": 20654.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 775907445, "mappedReadsCount": 457089602, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138860" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002543", "name": "vein endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_venous_systemic, Vascular", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 13.223659, "sdRefIntergenicDistribution": 1.438955, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 83846, "distinctRankCount": 2100, "maxRank": 22240.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 775907445, "mappedReadsCount": 457089602, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138860" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0009089", "name": "lung pericyte" }, "cellTypeAuthorAnnotation": "Muscle_pericyte_pulmonary, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 93.947824, "sdRefIntergenicDistribution": 1.278590, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 10665, "distinctRankCount": 622, "maxRank": 19353.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 775907445, "mappedReadsCount": 457089602, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138860" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000814", "name": "mature NK T cell" }, "cellTypeAuthorAnnotation": "NKT, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 40.170633, "sdRefIntergenicDistribution": 1.361809, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 25950, "distinctRankCount": 1087, "maxRank": 20733.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 775907445, "mappedReadsCount": 457089602, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138860" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000160", "name": "goblet cell" }, "cellTypeAuthorAnnotation": "Secretory_Goblet, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 3.455403, "sdRefIntergenicDistribution": 1.911992, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 426017, "distinctRankCount": 4178, "maxRank": 25055.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 775907445, "mappedReadsCount": 457089602, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138860" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000940", "name": "mucosal invariant T cell" }, "cellTypeAuthorAnnotation": "MAIT, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 94.798495, "sdRefIntergenicDistribution": 1.224675, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 10459, "distinctRankCount": 573, "maxRank": 19404.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 775907445, "mappedReadsCount": 457089602, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138860" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000319", "name": "mucus secreting cell" }, "cellTypeAuthorAnnotation": "SMG_Mucous, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 1.587958, "sdRefIntergenicDistribution": 2.227719, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1262618, "distinctRankCount": 5128, "maxRank": 26585.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 775907445, "mappedReadsCount": 457089602, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138860" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:1001568", "name": "pulmonary artery endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_arterial_pulmonary, Vascular", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 20.803685, "sdRefIntergenicDistribution": 1.436334, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 51496, "distinctRankCount": 1700, "maxRank": 21592.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 775907445, "mappedReadsCount": 457089602, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138860" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000185", "name": "myoepithelial cell" }, "cellTypeAuthorAnnotation": "Myoepithelial, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 20.530078, "sdRefIntergenicDistribution": 1.387279, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 52341, "distinctRankCount": 1923, "maxRank": 21574.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 775907445, "mappedReadsCount": 457089602, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138860" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000798", "name": "gamma-delta T cell" }, "cellTypeAuthorAnnotation": "gdT, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 20.967286, "sdRefIntergenicDistribution": 1.491873, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 51818, "distinctRankCount": 1570, "maxRank": 21590.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 775907445, "mappedReadsCount": 457089602, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138860" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0017000", "name": "pulmonary ionocyte" }, "cellTypeAuthorAnnotation": "Ionocyte_n_Brush, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 112.075620, "sdRefIntergenicDistribution": 1.243292, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 8925, "distinctRankCount": 535, "maxRank": 19184.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 775907445, "mappedReadsCount": 457089602, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138860" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000788", "name": "naive B cell" }, "cellTypeAuthorAnnotation": "B_naive, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 67.001655, "sdRefIntergenicDistribution": 1.317517, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 14919, "distinctRankCount": 758, "maxRank": 19880.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 775907445, "mappedReadsCount": 457089602, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138860" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000235", "name": "macrophage" }, "cellTypeAuthorAnnotation": "Macro_AW_CX3CR1, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 30.461318, "sdRefIntergenicDistribution": 1.362673, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 34073, "distinctRankCount": 1313, "maxRank": 21052.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 775907445, "mappedReadsCount": 457089602, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138860" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000987", "name": "IgA plasma cell" }, "cellTypeAuthorAnnotation": "B_plasma_IgA, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 10.727931, "sdRefIntergenicDistribution": 1.643038, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 109778, "distinctRankCount": 2221, "maxRank": 22773.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 775907445, "mappedReadsCount": 457089602, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138860" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000057", "name": "fibroblast" }, "cellTypeAuthorAnnotation": "NAF_endoneurial, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 194.370009, "sdRefIntergenicDistribution": 1.194896, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 4938, "distinctRankCount": 210, "maxRank": 18594.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 775907445, "mappedReadsCount": 457089602, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138860" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000057", "name": "fibroblast" }, "cellTypeAuthorAnnotation": "NAF_perineurial, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 24.380198, "sdRefIntergenicDistribution": 1.395819, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 43678, "distinctRankCount": 1509, "maxRank": 21127.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 775907445, "mappedReadsCount": 457089602, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138860" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002376", "name": "non-myelinating Schwann cell" }, "cellTypeAuthorAnnotation": "Schwann_nonmyelinating, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 35.965723, "sdRefIntergenicDistribution": 1.322964, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 28636, "distinctRankCount": 1294, "maxRank": 20624.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 775907445, "mappedReadsCount": 457089602, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138860" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000787", "name": "memory B cell" }, "cellTypeAuthorAnnotation": "B_memory, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 22.764964, "sdRefIntergenicDistribution": 1.447367, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 46734, "distinctRankCount": 1611, "maxRank": 21532.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 775907445, "mappedReadsCount": 457089602, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138860" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000138", "name": "chondrocyte" }, "cellTypeAuthorAnnotation": "Chondrocyte, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 2.711677, "sdRefIntergenicDistribution": 1.953010, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 581997, "distinctRankCount": 4061, "maxRank": 25583.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 775907445, "mappedReadsCount": 457089602, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138860" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002368", "name": "respiratory epithelial cell" }, "cellTypeAuthorAnnotation": "Suprabasal, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 3.750684, "sdRefIntergenicDistribution": 1.837588, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 378342, "distinctRankCount": 3848, "maxRank": 24976.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 775907445, "mappedReadsCount": 457089602, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138860" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000165", "name": "neuroendocrine cell" }, "cellTypeAuthorAnnotation": "Neuroendocrine, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 36.254924, "sdRefIntergenicDistribution": 1.434535, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 29821, "distinctRankCount": 1586, "maxRank": 20389.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 775907445, "mappedReadsCount": 457089602, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138860" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000077", "name": "mesothelial cell" }, "cellTypeAuthorAnnotation": "Mesothelia, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 120.336251, "sdRefIntergenicDistribution": 1.345947, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 8384, "distinctRankCount": 516, "maxRank": 18903.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 775907445, "mappedReadsCount": 457089602, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138860" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:1000413", "name": "endothelial cell of artery" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_arterial_systemic, Vascular", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 116.019424, "sdRefIntergenicDistribution": 1.413204, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 8967, "distinctRankCount": 531, "maxRank": 19033.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 775907445, "mappedReadsCount": 457089602, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138860" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000784", "name": "plasmacytoid dendritic cell" }, "cellTypeAuthorAnnotation": "DC_plasmacytoid, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 283.695536, "sdRefIntergenicDistribution": 1.242586, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 3419, "distinctRankCount": 145, "maxRank": 18424.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 775907445, "mappedReadsCount": 457089602, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138860" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002062", "name": "type I pneumocyte" }, "cellTypeAuthorAnnotation": "AT1 , Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 1.718872, "sdRefIntergenicDistribution": 2.250237, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1129676, "distinctRankCount": 4899, "maxRank": 26673.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 775907445, "mappedReadsCount": 457089602, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138860" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:4033044", "name": "deuterosomal cell" }, "cellTypeAuthorAnnotation": "Deuterosomal, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 15.400471, "sdRefIntergenicDistribution": 1.629498, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 76017, "distinctRankCount": 2453, "maxRank": 21860.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 775907445, "mappedReadsCount": 457089602, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138860" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000218", "name": "myelinating Schwann cell" }, "cellTypeAuthorAnnotation": "Schwann_Myelinating, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 427.847931, "sdRefIntergenicDistribution": 1.247034, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 2304, "distinctRankCount": 86, "maxRank": 18135.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 775907445, "mappedReadsCount": 457089602, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138860" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000669", "name": "pericyte cell" }, "cellTypeAuthorAnnotation": "Muscle_pericyte_systemic, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 153.509055, "sdRefIntergenicDistribution": 1.179701, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 6426, "distinctRankCount": 366, "maxRank": 18756.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 775907445, "mappedReadsCount": 457089602, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138860" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000980", "name": "plasmablast" }, "cellTypeAuthorAnnotation": "B_plasmablast, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 249.778031, "sdRefIntergenicDistribution": 1.399179, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 3465, "distinctRankCount": 333, "maxRank": 18458.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 967782639, "mappedReadsCount": 568525239, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138868" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002144", "name": "capillary endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_Cap_a, Vascular", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 5.245792, "sdRefIntergenicDistribution": 1.765283, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 250546, "distinctRankCount": 3020, "maxRank": 24528.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 967782639, "mappedReadsCount": 568525239, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138868" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002144", "name": "capillary endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_Cap_g, Vascular", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 4.030259, "sdRefIntergenicDistribution": 1.875645, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 352914, "distinctRankCount": 3285, "maxRank": 25021.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 967782639, "mappedReadsCount": 568525239, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138868" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000067", "name": "ciliated epithelial cell" }, "cellTypeAuthorAnnotation": "Ciliated, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 3.538962, "sdRefIntergenicDistribution": 2.141301, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 454298, "distinctRankCount": 4391, "maxRank": 25309.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 967782639, "mappedReadsCount": 568525239, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138868" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002396", "name": "CD14-low, CD16-positive monocyte" }, "cellTypeAuthorAnnotation": "Monocyte_CD16, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 6.715272, "sdRefIntergenicDistribution": 1.605783, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 179584, "distinctRankCount": 2736, "maxRank": 23828.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 967782639, "mappedReadsCount": 568525239, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138868" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000909", "name": "CD8-positive, alpha-beta memory T cell" }, "cellTypeAuthorAnnotation": "CD8_TRM, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 4.247875, "sdRefIntergenicDistribution": 1.753793, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 314024, "distinctRankCount": 3153, "maxRank": 24796.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 967782639, "mappedReadsCount": 568525239, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138868" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000909", "name": "CD8-positive, alpha-beta memory T cell" }, "cellTypeAuthorAnnotation": "CD8_TRM/EM, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 11.147402, "sdRefIntergenicDistribution": 1.560411, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 102325, "distinctRankCount": 2055, "maxRank": 22667.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 967782639, "mappedReadsCount": 568525239, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138868" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000897", "name": "CD4-positive, alpha-beta memory T cell" }, "cellTypeAuthorAnnotation": "CD4_TRM, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 53.056970, "sdRefIntergenicDistribution": 1.344511, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 19642, "distinctRankCount": 879, "maxRank": 20209.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 967782639, "mappedReadsCount": 568525239, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138868" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000146", "name": "simple columnar epithelial cell" }, "cellTypeAuthorAnnotation": "SMG_Duct, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 10.016005, "sdRefIntergenicDistribution": 1.556745, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 115600, "distinctRankCount": 2586, "maxRank": 22909.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 967782639, "mappedReadsCount": 568525239, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138868" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000097", "name": "mast cell" }, "cellTypeAuthorAnnotation": "Mast_cell , Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 10.558410, "sdRefIntergenicDistribution": 1.628104, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 111173, "distinctRankCount": 2346, "maxRank": 22902.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 967782639, "mappedReadsCount": 568525239, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138868" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002633", "name": "respiratory basal cell" }, "cellTypeAuthorAnnotation": "Basal, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 5.501754, "sdRefIntergenicDistribution": 1.726314, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 233225, "distinctRankCount": 3368, "maxRank": 24523.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 967782639, "mappedReadsCount": 568525239, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138868" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002633", "name": "respiratory basal cell" }, "cellTypeAuthorAnnotation": "Dividing_Basal, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 65.596671, "sdRefIntergenicDistribution": 1.303199, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 15610, "distinctRankCount": 956, "maxRank": 19874.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 967782639, "mappedReadsCount": 568525239, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138868" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002633", "name": "respiratory basal cell" }, "cellTypeAuthorAnnotation": "SMG_Basal, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 574.615035, "sdRefIntergenicDistribution": 1.030841, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1747, "distinctRankCount": 39, "maxRank": 18118.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 967782639, "mappedReadsCount": 568525239, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138868" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000624", "name": "CD4-positive, alpha-beta T cell" }, "cellTypeAuthorAnnotation": "CD4_EM/Effector, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 4.780435, "sdRefIntergenicDistribution": 1.701656, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 270120, "distinctRankCount": 2913, "maxRank": 24602.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 967782639, "mappedReadsCount": 568525239, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138868" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000624", "name": "CD4-positive, alpha-beta T cell" }, "cellTypeAuthorAnnotation": "CD4_naive/CM, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 4.477520, "sdRefIntergenicDistribution": 1.739395, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 294112, "distinctRankCount": 3137, "maxRank": 24671.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 967782639, "mappedReadsCount": 568525239, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138868" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000583", "name": "alveolar macrophage" }, "cellTypeAuthorAnnotation": "Macro_alveolar, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 3.888081, "sdRefIntergenicDistribution": 1.882285, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 363062, "distinctRankCount": 3855, "maxRank": 24915.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 967782639, "mappedReadsCount": 568525239, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138868" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000583", "name": "alveolar macrophage" }, "cellTypeAuthorAnnotation": "Macro_alveolar_metallothioneins, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 1308.676511, "sdRefIntergenicDistribution": 1.010969, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 725, "distinctRankCount": 25, "maxRank": 17832.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 967782639, "mappedReadsCount": 568525239, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138868" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000815", "name": "regulatory T cell" }, "cellTypeAuthorAnnotation": "T_reg, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 17.632127, "sdRefIntergenicDistribution": 1.445510, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 61826, "distinctRankCount": 1755, "maxRank": 21898.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 967782639, "mappedReadsCount": 568525239, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138868" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002553", "name": "fibroblast of lung" }, "cellTypeAuthorAnnotation": "Fibro_adventitial, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 2.279046, "sdRefIntergenicDistribution": 2.103073, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 819581, "distinctRankCount": 4654, "maxRank": 26472.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 967782639, "mappedReadsCount": 568525239, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138868" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002553", "name": "fibroblast of lung" }, "cellTypeAuthorAnnotation": "Fibro_alveolar, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 1.576447, "sdRefIntergenicDistribution": 2.392636, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1539166, "distinctRankCount": 5596, "maxRank": 27134.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 967782639, "mappedReadsCount": 568525239, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138868" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002553", "name": "fibroblast of lung" }, "cellTypeAuthorAnnotation": "Fibro_peribronchial, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 5.896191, "sdRefIntergenicDistribution": 1.641130, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 209407, "distinctRankCount": 3271, "maxRank": 24120.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 967782639, "mappedReadsCount": 568525239, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138868" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002553", "name": "fibroblast of lung" }, "cellTypeAuthorAnnotation": "Fibro_perichondrial, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 22.883572, "sdRefIntergenicDistribution": 1.423950, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 46916, "distinctRankCount": 1718, "maxRank": 21105.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 967782639, "mappedReadsCount": 568525239, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138868" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:1001603", "name": "lung macrophage" }, "cellTypeAuthorAnnotation": "Macro_CHIT1, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 29.798746, "sdRefIntergenicDistribution": 1.371228, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 35152, "distinctRankCount": 1467, "maxRank": 20837.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 967782639, "mappedReadsCount": 568525239, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138868" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:1001603", "name": "lung macrophage" }, "cellTypeAuthorAnnotation": "Macro_intermediate, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 38.074214, "sdRefIntergenicDistribution": 1.313048, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 26926, "distinctRankCount": 1110, "maxRank": 20453.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 967782639, "mappedReadsCount": 568525239, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138868" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:1001603", "name": "lung macrophage" }, "cellTypeAuthorAnnotation": "Macro_interstitial, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 143.315532, "sdRefIntergenicDistribution": 1.309369, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 6840, "distinctRankCount": 385, "maxRank": 18892.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 967782639, "mappedReadsCount": 568525239, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138868" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:1001603", "name": "lung macrophage" }, "cellTypeAuthorAnnotation": "Macro_intravascular, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 15.606663, "sdRefIntergenicDistribution": 1.469250, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 70170, "distinctRankCount": 1912, "maxRank": 22107.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 967782639, "mappedReadsCount": 568525239, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138868" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000623", "name": "natural killer cell" }, "cellTypeAuthorAnnotation": "NK_CD11d, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 14.759646, "sdRefIntergenicDistribution": 1.560352, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 77279, "distinctRankCount": 1911, "maxRank": 22396.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 967782639, "mappedReadsCount": 568525239, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138868" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000623", "name": "natural killer cell" }, "cellTypeAuthorAnnotation": "NK_CD16hi, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 4.085531, "sdRefIntergenicDistribution": 1.780020, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 325328, "distinctRankCount": 2983, "maxRank": 25053.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 967782639, "mappedReadsCount": 568525239, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138868" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000623", "name": "natural killer cell" }, "cellTypeAuthorAnnotation": "NK_CD56bright, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 138.606050, "sdRefIntergenicDistribution": 1.355150, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 7589, "distinctRankCount": 455, "maxRank": 18923.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 967782639, "mappedReadsCount": 568525239, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138868" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000985", "name": "IgG plasma cell" }, "cellTypeAuthorAnnotation": "B_plasma_IgG, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 14.972712, "sdRefIntergenicDistribution": 1.650844, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 76225, "distinctRankCount": 1979, "maxRank": 22091.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 967782639, "mappedReadsCount": 568525239, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138868" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0009115", "name": "lymph node lymphatic vessel endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_Lymphatic, Vascular", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 6.245071, "sdRefIntergenicDistribution": 1.636047, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 196717, "distinctRankCount": 3036, "maxRank": 24313.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 967782639, "mappedReadsCount": 568525239, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138868" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000913", "name": "effector memory CD8-positive, alpha-beta T cell" }, "cellTypeAuthorAnnotation": "CD8_EM, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 13.856120, "sdRefIntergenicDistribution": 1.464859, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 79897, "distinctRankCount": 1815, "maxRank": 22216.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 967782639, "mappedReadsCount": 568525239, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138868" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000913", "name": "effector memory CD8-positive, alpha-beta T cell" }, "cellTypeAuthorAnnotation": "CD8_EM/EMRA, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 11.412728, "sdRefIntergenicDistribution": 1.527722, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 98725, "distinctRankCount": 2043, "maxRank": 22746.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 967782639, "mappedReadsCount": 568525239, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138868" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000186", "name": "myofibroblast cell" }, "cellTypeAuthorAnnotation": "Fibro_myofibroblast, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 19.098181, "sdRefIntergenicDistribution": 1.405444, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 56220, "distinctRankCount": 1810, "maxRank": 21865.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 967782639, "mappedReadsCount": 568525239, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138868" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000158", "name": "club cell" }, "cellTypeAuthorAnnotation": "Secretory_Club, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 3.672983, "sdRefIntergenicDistribution": 1.796423, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 375684, "distinctRankCount": 3703, "maxRank": 24873.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 967782639, "mappedReadsCount": 568525239, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138868" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0001065", "name": "innate lymphoid cell" }, "cellTypeAuthorAnnotation": "ILC, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 176.755026, "sdRefIntergenicDistribution": 1.215557, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 5660, "distinctRankCount": 328, "maxRank": 18774.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 967782639, "mappedReadsCount": 568525239, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138868" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000192", "name": "smooth muscle cell" }, "cellTypeAuthorAnnotation": "Muscle_smooth_pulmonary, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 13.040710, "sdRefIntergenicDistribution": 1.424335, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 84726, "distinctRankCount": 2122, "maxRank": 22208.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 967782639, "mappedReadsCount": 568525239, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138868" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0019001", "name": "tracheobronchial serous cell" }, "cellTypeAuthorAnnotation": "SMG_Serous, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 1.208479, "sdRefIntergenicDistribution": 2.558749, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 2424939, "distinctRankCount": 6226, "maxRank": 27335.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 967782639, "mappedReadsCount": 568525239, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138868" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0019019", "name": "tracheobronchial smooth muscle cell" }, "cellTypeAuthorAnnotation": "Muscle_smooth_airway, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 10.930448, "sdRefIntergenicDistribution": 1.457327, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 102903, "distinctRankCount": 2181, "maxRank": 21982.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 967782639, "mappedReadsCount": 568525239, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138868" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000990", "name": "conventional dendritic cell" }, "cellTypeAuthorAnnotation": "DC_1, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 67.293212, "sdRefIntergenicDistribution": 1.313376, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 14864, "distinctRankCount": 845, "maxRank": 19520.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 967782639, "mappedReadsCount": 568525239, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138868" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000990", "name": "conventional dendritic cell" }, "cellTypeAuthorAnnotation": "DC_2, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 12.100458, "sdRefIntergenicDistribution": 1.485299, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 92216, "distinctRankCount": 2312, "maxRank": 22450.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 967782639, "mappedReadsCount": 568525239, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138868" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000990", "name": "conventional dendritic cell" }, "cellTypeAuthorAnnotation": "DC_activated, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 92.697314, "sdRefIntergenicDistribution": 1.397587, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 11368, "distinctRankCount": 555, "maxRank": 19023.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 967782639, "mappedReadsCount": 568525239, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138868" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0019018", "name": "blood vessel smooth muscle cell" }, "cellTypeAuthorAnnotation": "Muscle_perivascular_immune_recruiting, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 19.483234, "sdRefIntergenicDistribution": 1.379160, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 54216, "distinctRankCount": 1698, "maxRank": 21471.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 967782639, "mappedReadsCount": 568525239, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138868" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0019018", "name": "blood vessel smooth muscle cell" }, "cellTypeAuthorAnnotation": "Muscle_smooth_arterial_systemic, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 103.439949, "sdRefIntergenicDistribution": 1.317314, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 9679, "distinctRankCount": 455, "maxRank": 18967.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 967782639, "mappedReadsCount": 568525239, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138868" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0001054", "name": "CD14-positive monocyte" }, "cellTypeAuthorAnnotation": "Monocyte_CD14, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 7.087360, "sdRefIntergenicDistribution": 1.553493, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 164479, "distinctRankCount": 2770, "maxRank": 23767.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 967782639, "mappedReadsCount": 568525239, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138868" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002063", "name": "type II pneumocyte" }, "cellTypeAuthorAnnotation": "AT2, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 0.905044, "sdRefIntergenicDistribution": 2.979861, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 5363632, "distinctRankCount": 7166, "maxRank": 27899.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 967782639, "mappedReadsCount": 568525239, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138868" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002543", "name": "vein endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_venous_pulmonary, Vascular", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 15.487266, "sdRefIntergenicDistribution": 1.504957, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 71391, "distinctRankCount": 2101, "maxRank": 21989.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 967782639, "mappedReadsCount": 568525239, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138868" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002543", "name": "vein endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_venous_systemic, Vascular", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 15.716076, "sdRefIntergenicDistribution": 1.437557, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 68634, "distinctRankCount": 1955, "maxRank": 21976.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 967782639, "mappedReadsCount": 568525239, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138868" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0009089", "name": "lung pericyte" }, "cellTypeAuthorAnnotation": "Muscle_pericyte_pulmonary, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 21.573470, "sdRefIntergenicDistribution": 1.433269, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 50229, "distinctRankCount": 1704, "maxRank": 21316.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 967782639, "mappedReadsCount": 568525239, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138868" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000814", "name": "mature NK T cell" }, "cellTypeAuthorAnnotation": "NKT, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 19.428098, "sdRefIntergenicDistribution": 1.406773, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 54062, "distinctRankCount": 1599, "maxRank": 21946.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 967782639, "mappedReadsCount": 568525239, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138868" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000160", "name": "goblet cell" }, "cellTypeAuthorAnnotation": "Secretory_Goblet, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 2.072440, "sdRefIntergenicDistribution": 2.162083, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 894629, "distinctRankCount": 5280, "maxRank": 26186.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 967782639, "mappedReadsCount": 568525239, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138868" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000940", "name": "mucosal invariant T cell" }, "cellTypeAuthorAnnotation": "MAIT, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 31.411194, "sdRefIntergenicDistribution": 1.419501, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 34016, "distinctRankCount": 1209, "maxRank": 20875.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 967782639, "mappedReadsCount": 568525239, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138868" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000319", "name": "mucus secreting cell" }, "cellTypeAuthorAnnotation": "SMG_Mucous, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 0.885798, "sdRefIntergenicDistribution": 2.956764, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 5773211, "distinctRankCount": 7777, "maxRank": 28168.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 967782639, "mappedReadsCount": 568525239, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138868" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:1001568", "name": "pulmonary artery endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_arterial_pulmonary, Vascular", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 14.544171, "sdRefIntergenicDistribution": 1.492170, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 76468, "distinctRankCount": 1952, "maxRank": 22175.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 967782639, "mappedReadsCount": 568525239, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138868" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000185", "name": "myoepithelial cell" }, "cellTypeAuthorAnnotation": "Myoepithelial, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 32.794716, "sdRefIntergenicDistribution": 1.364899, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 32089, "distinctRankCount": 1411, "maxRank": 20770.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 967782639, "mappedReadsCount": 568525239, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138868" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000798", "name": "gamma-delta T cell" }, "cellTypeAuthorAnnotation": "gdT, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 42.488794, "sdRefIntergenicDistribution": 1.340109, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 24454, "distinctRankCount": 1103, "maxRank": 20313.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 967782639, "mappedReadsCount": 568525239, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138868" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000788", "name": "naive B cell" }, "cellTypeAuthorAnnotation": "B_naive, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 33.607792, "sdRefIntergenicDistribution": 1.407693, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 31140, "distinctRankCount": 1248, "maxRank": 20838.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 967782639, "mappedReadsCount": 568525239, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138868" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000235", "name": "macrophage" }, "cellTypeAuthorAnnotation": "Macro_AW_CX3CR1, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 50.095632, "sdRefIntergenicDistribution": 1.321254, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 20603, "distinctRankCount": 1149, "maxRank": 20168.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 967782639, "mappedReadsCount": 568525239, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138868" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000987", "name": "IgA plasma cell" }, "cellTypeAuthorAnnotation": "B_plasma_IgA, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 12.132772, "sdRefIntergenicDistribution": 1.677867, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 97988, "distinctRankCount": 2296, "maxRank": 22538.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 967782639, "mappedReadsCount": 568525239, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138868" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000057", "name": "fibroblast" }, "cellTypeAuthorAnnotation": "NAF_endoneurial, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 562.221102, "sdRefIntergenicDistribution": 1.111217, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1716, "distinctRankCount": 84, "maxRank": 18022.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 967782639, "mappedReadsCount": 568525239, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138868" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000057", "name": "fibroblast" }, "cellTypeAuthorAnnotation": "NAF_perineurial, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 733.619707, "sdRefIntergenicDistribution": 1.115727, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1273, "distinctRankCount": 32, "maxRank": 17894.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 967782639, "mappedReadsCount": 568525239, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138868" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002376", "name": "non-myelinating Schwann cell" }, "cellTypeAuthorAnnotation": "Schwann_nonmyelinating, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 47.415918, "sdRefIntergenicDistribution": 1.318896, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 21627, "distinctRankCount": 1245, "maxRank": 20037.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 967782639, "mappedReadsCount": 568525239, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138868" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000787", "name": "memory B cell" }, "cellTypeAuthorAnnotation": "B_memory, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 27.677557, "sdRefIntergenicDistribution": 1.459015, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 38864, "distinctRankCount": 1423, "maxRank": 21036.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 967782639, "mappedReadsCount": 568525239, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138868" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000138", "name": "chondrocyte" }, "cellTypeAuthorAnnotation": "Chondrocyte, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 17.987546, "sdRefIntergenicDistribution": 1.468815, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 60640, "distinctRankCount": 2030, "maxRank": 21618.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 967782639, "mappedReadsCount": 568525239, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138868" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002368", "name": "respiratory epithelial cell" }, "cellTypeAuthorAnnotation": "Suprabasal, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 6.771801, "sdRefIntergenicDistribution": 1.666467, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 180656, "distinctRankCount": 3526, "maxRank": 23825.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 967782639, "mappedReadsCount": 568525239, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138868" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000165", "name": "neuroendocrine cell" }, "cellTypeAuthorAnnotation": "Neuroendocrine, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 778.036989, "sdRefIntergenicDistribution": 1.134724, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1252, "distinctRankCount": 56, "maxRank": 17978.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 967782639, "mappedReadsCount": 568525239, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138868" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000077", "name": "mesothelial cell" }, "cellTypeAuthorAnnotation": "Mesothelia, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 241.571233, "sdRefIntergenicDistribution": 1.208748, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 3838, "distinctRankCount": 266, "maxRank": 18321.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 967782639, "mappedReadsCount": 568525239, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138868" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:1000413", "name": "endothelial cell of artery" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_arterial_systemic, Vascular", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 152.485076, "sdRefIntergenicDistribution": 1.420708, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 6693, "distinctRankCount": 367, "maxRank": 18763.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 967782639, "mappedReadsCount": 568525239, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138868" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002062", "name": "type I pneumocyte" }, "cellTypeAuthorAnnotation": "AT1 , Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 1.640880, "sdRefIntergenicDistribution": 2.408091, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1358215, "distinctRankCount": 5302, "maxRank": 26653.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 967782639, "mappedReadsCount": 568525239, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138868" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000669", "name": "pericyte cell" }, "cellTypeAuthorAnnotation": "Muscle_pericyte_systemic, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 167.955847, "sdRefIntergenicDistribution": 1.281211, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 6003, "distinctRankCount": 371, "maxRank": 18688.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937076228, "mappedReadsCount": 561863245, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138871" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002144", "name": "capillary endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_Cap_a, Vascular", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 24.430259, "sdRefIntergenicDistribution": 1.341248, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 42056, "distinctRankCount": 1497, "maxRank": 21511.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937076228, "mappedReadsCount": 561863245, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138871" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002144", "name": "capillary endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_Cap_g, Vascular", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 11.356297, "sdRefIntergenicDistribution": 1.496383, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 98477, "distinctRankCount": 2201, "maxRank": 22777.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937076228, "mappedReadsCount": 561863245, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138871" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000067", "name": "ciliated epithelial cell" }, "cellTypeAuthorAnnotation": "Ciliated, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 8.906675, "sdRefIntergenicDistribution": 1.898180, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 146291, "distinctRankCount": 3013, "maxRank": 23380.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937076228, "mappedReadsCount": 561863245, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138871" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002396", "name": "CD14-low, CD16-positive monocyte" }, "cellTypeAuthorAnnotation": "Monocyte_CD16, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 13.854870, "sdRefIntergenicDistribution": 1.423159, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 77718, "distinctRankCount": 2058, "maxRank": 22224.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937076228, "mappedReadsCount": 561863245, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138871" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000909", "name": "CD8-positive, alpha-beta memory T cell" }, "cellTypeAuthorAnnotation": "CD8_TRM, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 15.714928, "sdRefIntergenicDistribution": 1.458675, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 69335, "distinctRankCount": 1975, "maxRank": 21986.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937076228, "mappedReadsCount": 561863245, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138871" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000909", "name": "CD8-positive, alpha-beta memory T cell" }, "cellTypeAuthorAnnotation": "CD8_TRM/EM, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 15.900273, "sdRefIntergenicDistribution": 1.451830, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 69660, "distinctRankCount": 1698, "maxRank": 21633.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937076228, "mappedReadsCount": 561863245, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138871" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000897", "name": "CD4-positive, alpha-beta memory T cell" }, "cellTypeAuthorAnnotation": "CD4_TRM, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 46.896027, "sdRefIntergenicDistribution": 1.686706, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 24409, "distinctRankCount": 1100, "maxRank": 20341.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937076228, "mappedReadsCount": 561863245, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138871" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000146", "name": "simple columnar epithelial cell" }, "cellTypeAuthorAnnotation": "SMG_Duct, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 8.312726, "sdRefIntergenicDistribution": 1.564131, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 141155, "distinctRankCount": 2741, "maxRank": 23038.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937076228, "mappedReadsCount": 561863245, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138871" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000097", "name": "mast cell" }, "cellTypeAuthorAnnotation": "Mast_cell , Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 52.117430, "sdRefIntergenicDistribution": 1.348924, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 19243, "distinctRankCount": 961, "maxRank": 19906.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937076228, "mappedReadsCount": 561863245, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138871" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002633", "name": "respiratory basal cell" }, "cellTypeAuthorAnnotation": "Basal, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 12.458462, "sdRefIntergenicDistribution": 1.498634, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 90083, "distinctRankCount": 2451, "maxRank": 22300.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937076228, "mappedReadsCount": 561863245, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138871" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002633", "name": "respiratory basal cell" }, "cellTypeAuthorAnnotation": "Dividing_Basal, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 159.641316, "sdRefIntergenicDistribution": 1.271004, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 6017, "distinctRankCount": 412, "maxRank": 18829.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937076228, "mappedReadsCount": 561863245, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138871" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000624", "name": "CD4-positive, alpha-beta T cell" }, "cellTypeAuthorAnnotation": "CD4_EM/Effector, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 7.267941, "sdRefIntergenicDistribution": 1.571732, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 161103, "distinctRankCount": 2544, "maxRank": 23648.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937076228, "mappedReadsCount": 561863245, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138871" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000624", "name": "CD4-positive, alpha-beta T cell" }, "cellTypeAuthorAnnotation": "CD4_naive/CM, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 10.561069, "sdRefIntergenicDistribution": 1.517688, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 106087, "distinctRankCount": 2087, "maxRank": 22880.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937076228, "mappedReadsCount": 561863245, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138871" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000583", "name": "alveolar macrophage" }, "cellTypeAuthorAnnotation": "Macro_alveolar, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 10.879884, "sdRefIntergenicDistribution": 1.633526, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 109226, "distinctRankCount": 2670, "maxRank": 22852.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937076228, "mappedReadsCount": 561863245, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138871" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000815", "name": "regulatory T cell" }, "cellTypeAuthorAnnotation": "T_reg, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 47.987791, "sdRefIntergenicDistribution": 1.325212, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 21360, "distinctRankCount": 937, "maxRank": 20212.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937076228, "mappedReadsCount": 561863245, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138871" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002553", "name": "fibroblast of lung" }, "cellTypeAuthorAnnotation": "Fibro_adventitial, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 3.968672, "sdRefIntergenicDistribution": 1.784797, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 342910, "distinctRankCount": 3640, "maxRank": 25250.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937076228, "mappedReadsCount": 561863245, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138871" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002553", "name": "fibroblast of lung" }, "cellTypeAuthorAnnotation": "Fibro_alveolar, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 2.747242, "sdRefIntergenicDistribution": 2.010216, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 587500, "distinctRankCount": 4178, "maxRank": 25875.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937076228, "mappedReadsCount": 561863245, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138871" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002553", "name": "fibroblast of lung" }, "cellTypeAuthorAnnotation": "Fibro_peribronchial, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 50.444121, "sdRefIntergenicDistribution": 1.273090, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 19559, "distinctRankCount": 1068, "maxRank": 20184.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937076228, "mappedReadsCount": 561863245, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138871" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002553", "name": "fibroblast of lung" }, "cellTypeAuthorAnnotation": "Fibro_perichondrial, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 22.514387, "sdRefIntergenicDistribution": 1.459472, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 48251, "distinctRankCount": 1940, "maxRank": 21060.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937076228, "mappedReadsCount": 561863245, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138871" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:1001603", "name": "lung macrophage" }, "cellTypeAuthorAnnotation": "Macro_CCL, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 212.556250, "sdRefIntergenicDistribution": 1.236005, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 4664, "distinctRankCount": 206, "maxRank": 18273.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937076228, "mappedReadsCount": 561863245, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138871" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:1001603", "name": "lung macrophage" }, "cellTypeAuthorAnnotation": "Macro_CHIT1, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 143.841450, "sdRefIntergenicDistribution": 1.204959, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 6601, "distinctRankCount": 340, "maxRank": 18858.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937076228, "mappedReadsCount": 561863245, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138871" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:1001603", "name": "lung macrophage" }, "cellTypeAuthorAnnotation": "Macro_intermediate, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 58.721857, "sdRefIntergenicDistribution": 1.328288, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 17459, "distinctRankCount": 911, "maxRank": 19903.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937076228, "mappedReadsCount": 561863245, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138871" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:1001603", "name": "lung macrophage" }, "cellTypeAuthorAnnotation": "Macro_intravascular, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 19.753506, "sdRefIntergenicDistribution": 1.415750, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 53471, "distinctRankCount": 1687, "maxRank": 21596.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937076228, "mappedReadsCount": 561863245, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138871" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000623", "name": "natural killer cell" }, "cellTypeAuthorAnnotation": "NK_CD11d, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 55.310963, "sdRefIntergenicDistribution": 1.372086, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 18651, "distinctRankCount": 935, "maxRank": 20165.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937076228, "mappedReadsCount": 561863245, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138871" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000623", "name": "natural killer cell" }, "cellTypeAuthorAnnotation": "NK_CD16hi, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 7.892321, "sdRefIntergenicDistribution": 1.616592, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 147562, "distinctRankCount": 2444, "maxRank": 23638.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937076228, "mappedReadsCount": 561863245, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138871" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000623", "name": "natural killer cell" }, "cellTypeAuthorAnnotation": "NK_CD56bright, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 222.648357, "sdRefIntergenicDistribution": 1.213747, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 4392, "distinctRankCount": 298, "maxRank": 18528.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937076228, "mappedReadsCount": 561863245, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138871" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000985", "name": "IgG plasma cell" }, "cellTypeAuthorAnnotation": "B_plasma_IgG, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 22.694044, "sdRefIntergenicDistribution": 1.543261, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 48906, "distinctRankCount": 1802, "maxRank": 21114.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937076228, "mappedReadsCount": 561863245, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138871" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0009115", "name": "lymph node lymphatic vessel endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_Lymphatic, Vascular", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 12.378073, "sdRefIntergenicDistribution": 1.434444, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 86202, "distinctRankCount": 2179, "maxRank": 22750.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937076228, "mappedReadsCount": 561863245, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138871" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000913", "name": "effector memory CD8-positive, alpha-beta T cell" }, "cellTypeAuthorAnnotation": "CD8_EM, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 20.995313, "sdRefIntergenicDistribution": 1.385015, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 50459, "distinctRankCount": 1591, "maxRank": 21448.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937076228, "mappedReadsCount": 561863245, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138871" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000913", "name": "effector memory CD8-positive, alpha-beta T cell" }, "cellTypeAuthorAnnotation": "CD8_EM/EMRA, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 17.338674, "sdRefIntergenicDistribution": 1.449405, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 61998, "distinctRankCount": 1625, "maxRank": 21882.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937076228, "mappedReadsCount": 561863245, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138871" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000186", "name": "myofibroblast cell" }, "cellTypeAuthorAnnotation": "Fibro_myofibroblast, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 114.473865, "sdRefIntergenicDistribution": 1.448959, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 9040, "distinctRankCount": 547, "maxRank": 18906.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937076228, "mappedReadsCount": 561863245, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138871" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000158", "name": "club cell" }, "cellTypeAuthorAnnotation": "Secretory_Club, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 4.059873, "sdRefIntergenicDistribution": 1.832686, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 345399, "distinctRankCount": 3566, "maxRank": 24980.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937076228, "mappedReadsCount": 561863245, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138871" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0001065", "name": "innate lymphoid cell" }, "cellTypeAuthorAnnotation": "ILC, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 1205.720619, "sdRefIntergenicDistribution": 1.221109, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 829, "distinctRankCount": 42, "maxRank": 17801.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937076228, "mappedReadsCount": 561863245, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138871" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000192", "name": "smooth muscle cell" }, "cellTypeAuthorAnnotation": "Muscle_smooth_pulmonary, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 14.203033, "sdRefIntergenicDistribution": 1.433803, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 75004, "distinctRankCount": 2021, "maxRank": 22237.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937076228, "mappedReadsCount": 561863245, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138871" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0019001", "name": "tracheobronchial serous cell" }, "cellTypeAuthorAnnotation": "SMG_Serous, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 1.054945, "sdRefIntergenicDistribution": 2.516017, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 2768265, "distinctRankCount": 6220, "maxRank": 27062.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937076228, "mappedReadsCount": 561863245, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138871" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0019019", "name": "tracheobronchial smooth muscle cell" }, "cellTypeAuthorAnnotation": "Muscle_smooth_airway, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 242.425867, "sdRefIntergenicDistribution": 1.231407, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 4014, "distinctRankCount": 303, "maxRank": 18452.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937076228, "mappedReadsCount": 561863245, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138871" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000990", "name": "conventional dendritic cell" }, "cellTypeAuthorAnnotation": "DC_1, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 322.627225, "sdRefIntergenicDistribution": 1.239563, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 3104, "distinctRankCount": 121, "maxRank": 18161.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937076228, "mappedReadsCount": 561863245, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138871" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000990", "name": "conventional dendritic cell" }, "cellTypeAuthorAnnotation": "DC_2, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 62.796558, "sdRefIntergenicDistribution": 1.350232, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 16817, "distinctRankCount": 892, "maxRank": 19629.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937076228, "mappedReadsCount": 561863245, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138871" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000990", "name": "conventional dendritic cell" }, "cellTypeAuthorAnnotation": "DC_activated, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 100.741347, "sdRefIntergenicDistribution": 1.327524, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 9933, "distinctRankCount": 688, "maxRank": 19122.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937076228, "mappedReadsCount": 561863245, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138871" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0019018", "name": "blood vessel smooth muscle cell" }, "cellTypeAuthorAnnotation": "Muscle_perivascular_immune_recruiting, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 40.399037, "sdRefIntergenicDistribution": 1.303893, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 25019, "distinctRankCount": 1127, "maxRank": 20100.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937076228, "mappedReadsCount": 561863245, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138871" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0019018", "name": "blood vessel smooth muscle cell" }, "cellTypeAuthorAnnotation": "Muscle_smooth_arterial_systemic, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 608.895364, "sdRefIntergenicDistribution": 1.186594, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1573, "distinctRankCount": 67, "maxRank": 18010.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937076228, "mappedReadsCount": 561863245, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138871" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0001054", "name": "CD14-positive monocyte" }, "cellTypeAuthorAnnotation": "Monocyte_CD14, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 52.673627, "sdRefIntergenicDistribution": 1.307337, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 18874, "distinctRankCount": 850, "maxRank": 20063.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937076228, "mappedReadsCount": 561863245, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138871" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002063", "name": "type II pneumocyte" }, "cellTypeAuthorAnnotation": "AT2, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 1.103186, "sdRefIntergenicDistribution": 2.671813, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 2962479, "distinctRankCount": 6326, "maxRank": 27400.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937076228, "mappedReadsCount": 561863245, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138871" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002063", "name": "type II pneumocyte" }, "cellTypeAuthorAnnotation": "Dividing_AT2, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 49.790103, "sdRefIntergenicDistribution": 1.374528, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 20488, "distinctRankCount": 1306, "maxRank": 20156.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937076228, "mappedReadsCount": 561863245, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138871" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002543", "name": "vein endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_venous_pulmonary, Vascular", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 28.210890, "sdRefIntergenicDistribution": 1.377744, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 36558, "distinctRankCount": 1536, "maxRank": 21074.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937076228, "mappedReadsCount": 561863245, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138871" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002543", "name": "vein endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_venous_systemic, Vascular", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 22.289281, "sdRefIntergenicDistribution": 1.339743, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 46649, "distinctRankCount": 1672, "maxRank": 21388.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937076228, "mappedReadsCount": 561863245, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138871" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0009089", "name": "lung pericyte" }, "cellTypeAuthorAnnotation": "Muscle_pericyte_pulmonary, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 91.057132, "sdRefIntergenicDistribution": 1.281131, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 10592, "distinctRankCount": 697, "maxRank": 19442.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937076228, "mappedReadsCount": 561863245, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138871" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000814", "name": "mature NK T cell" }, "cellTypeAuthorAnnotation": "NKT, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 49.056269, "sdRefIntergenicDistribution": 1.309692, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 20490, "distinctRankCount": 885, "maxRank": 20296.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937076228, "mappedReadsCount": 561863245, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138871" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000160", "name": "goblet cell" }, "cellTypeAuthorAnnotation": "Secretory_Goblet, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 8.126990, "sdRefIntergenicDistribution": 1.593501, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 146885, "distinctRankCount": 3112, "maxRank": 23162.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937076228, "mappedReadsCount": 561863245, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138871" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000940", "name": "mucosal invariant T cell" }, "cellTypeAuthorAnnotation": "MAIT, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 83.993413, "sdRefIntergenicDistribution": 1.220820, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 11926, "distinctRankCount": 601, "maxRank": 19412.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937076228, "mappedReadsCount": 561863245, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138871" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000319", "name": "mucus secreting cell" }, "cellTypeAuthorAnnotation": "SMG_Mucous, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 1.273034, "sdRefIntergenicDistribution": 2.295516, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1802844, "distinctRankCount": 5787, "maxRank": 26572.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937076228, "mappedReadsCount": 561863245, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138871" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:1001568", "name": "pulmonary artery endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_arterial_pulmonary, Vascular", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 40.042857, "sdRefIntergenicDistribution": 1.402322, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 26683, "distinctRankCount": 1219, "maxRank": 20532.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937076228, "mappedReadsCount": 561863245, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138871" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000185", "name": "myoepithelial cell" }, "cellTypeAuthorAnnotation": "Myoepithelial, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 4.022322, "sdRefIntergenicDistribution": 1.736573, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 335421, "distinctRankCount": 3581, "maxRank": 24386.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937076228, "mappedReadsCount": 561863245, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138871" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000798", "name": "gamma-delta T cell" }, "cellTypeAuthorAnnotation": "gdT, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 285.397421, "sdRefIntergenicDistribution": 1.225006, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 3370, "distinctRankCount": 192, "maxRank": 18284.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937076228, "mappedReadsCount": 561863245, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138871" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0017000", "name": "pulmonary ionocyte" }, "cellTypeAuthorAnnotation": "Ionocyte_n_Brush, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 186.487210, "sdRefIntergenicDistribution": 1.356167, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 5422, "distinctRankCount": 288, "maxRank": 18613.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937076228, "mappedReadsCount": 561863245, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138871" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000788", "name": "naive B cell" }, "cellTypeAuthorAnnotation": "B_naive, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 346.658219, "sdRefIntergenicDistribution": 1.001542, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 2565, "distinctRankCount": 92, "maxRank": 18261.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937076228, "mappedReadsCount": 561863245, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138871" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000235", "name": "macrophage" }, "cellTypeAuthorAnnotation": "Macro_AW_CX3CR1, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 43.688166, "sdRefIntergenicDistribution": 1.355273, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 23470, "distinctRankCount": 1280, "maxRank": 20298.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937076228, "mappedReadsCount": 561863245, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138871" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000987", "name": "IgA plasma cell" }, "cellTypeAuthorAnnotation": "B_plasma_IgA, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 7.739793, "sdRefIntergenicDistribution": 1.665514, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 157158, "distinctRankCount": 2552, "maxRank": 22932.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937076228, "mappedReadsCount": 561863245, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138871" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002376", "name": "non-myelinating Schwann cell" }, "cellTypeAuthorAnnotation": "Schwann_nonmyelinating, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 130.704592, "sdRefIntergenicDistribution": 1.297205, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 7727, "distinctRankCount": 447, "maxRank": 18837.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937076228, "mappedReadsCount": 561863245, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138871" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000787", "name": "memory B cell" }, "cellTypeAuthorAnnotation": "B_memory, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 114.844468, "sdRefIntergenicDistribution": 1.217114, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 7907, "distinctRankCount": 443, "maxRank": 19033.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937076228, "mappedReadsCount": 561863245, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138871" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000138", "name": "chondrocyte" }, "cellTypeAuthorAnnotation": "Chondrocyte, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 2.729721, "sdRefIntergenicDistribution": 2.050716, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 622126, "distinctRankCount": 4284, "maxRank": 25664.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937076228, "mappedReadsCount": 561863245, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138871" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002368", "name": "respiratory epithelial cell" }, "cellTypeAuthorAnnotation": "Suprabasal, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 70.529314, "sdRefIntergenicDistribution": 1.310019, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 14513, "distinctRankCount": 992, "maxRank": 19510.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937076228, "mappedReadsCount": 561863245, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138871" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000165", "name": "neuroendocrine cell" }, "cellTypeAuthorAnnotation": "Neuroendocrine, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 86.616193, "sdRefIntergenicDistribution": 1.317594, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 11633, "distinctRankCount": 837, "maxRank": 19355.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937076228, "mappedReadsCount": 561863245, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138871" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:1000413", "name": "endothelial cell of artery" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_arterial_systemic, Vascular", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 310.335797, "sdRefIntergenicDistribution": 1.163041, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 2949, "distinctRankCount": 179, "maxRank": 18291.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937076228, "mappedReadsCount": 561863245, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138871" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000784", "name": "plasmacytoid dendritic cell" }, "cellTypeAuthorAnnotation": "DC_plasmacytoid, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 181.844602, "sdRefIntergenicDistribution": 1.335962, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 5472, "distinctRankCount": 351, "maxRank": 18664.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937076228, "mappedReadsCount": 561863245, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138871" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002062", "name": "type I pneumocyte" }, "cellTypeAuthorAnnotation": "AT1 , Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 1.777384, "sdRefIntergenicDistribution": 2.329735, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1186408, "distinctRankCount": 5197, "maxRank": 26340.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937076228, "mappedReadsCount": 561863245, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138871" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000669", "name": "pericyte cell" }, "cellTypeAuthorAnnotation": "Muscle_pericyte_systemic, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 60.301896, "sdRefIntergenicDistribution": 1.301351, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 17059, "distinctRankCount": 811, "maxRank": 19405.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 937076228, "mappedReadsCount": 561863245, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138871" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000980", "name": "plasmablast" }, "cellTypeAuthorAnnotation": "B_plasmablast, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 127.060992, "sdRefIntergenicDistribution": 1.325347, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 7521, "distinctRankCount": 544, "maxRank": 19004.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 417307518, "mappedReadsCount": 235248718, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138875" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000319", "name": "mucus secreting cell" }, "cellTypeAuthorAnnotation": "SMG_Mucous, Epithelia", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 0.819020, "sdRefIntergenicDistribution": 3.004065, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 6838496, "distinctRankCount": 7887, "maxRank": 28134.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 417307518, "mappedReadsCount": 235248718, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138875" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000624", "name": "CD4-positive, alpha-beta T cell" }, "cellTypeAuthorAnnotation": "CD4_EM/Effector, Immune", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 16.819153, "sdRefIntergenicDistribution": 1.498846, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 65471, "distinctRankCount": 1781, "maxRank": 21769.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 417307518, "mappedReadsCount": 235248718, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138875" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000624", "name": "CD4-positive, alpha-beta T cell" }, "cellTypeAuthorAnnotation": "CD4_naive/CM, Immune", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 14.861785, "sdRefIntergenicDistribution": 1.524650, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 74920, "distinctRankCount": 1988, "maxRank": 22194.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 417307518, "mappedReadsCount": 235248718, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138875" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000185", "name": "myoepithelial cell" }, "cellTypeAuthorAnnotation": "Myoepithelial, Epithelia", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 3.323487, "sdRefIntergenicDistribution": 1.844996, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 443042, "distinctRankCount": 3999, "maxRank": 25264.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 417307518, "mappedReadsCount": 235248718, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138875" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000138", "name": "chondrocyte" }, "cellTypeAuthorAnnotation": "Chondrocyte, Stroma", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 1.711301, "sdRefIntergenicDistribution": 2.284331, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1224078, "distinctRankCount": 4966, "maxRank": 26467.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 417307518, "mappedReadsCount": 235248718, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138875" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0019019", "name": "tracheobronchial smooth muscle cell" }, "cellTypeAuthorAnnotation": "Muscle_smooth_airway, Stroma", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 2.242523, "sdRefIntergenicDistribution": 1.966112, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 743333, "distinctRankCount": 4241, "maxRank": 25316.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 417307518, "mappedReadsCount": 235248718, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138875" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000909", "name": "CD8-positive, alpha-beta memory T cell" }, "cellTypeAuthorAnnotation": "CD8_TRM, Immune", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 11.589485, "sdRefIntergenicDistribution": 1.550068, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 98864, "distinctRankCount": 2146, "maxRank": 22444.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 417307518, "mappedReadsCount": 235248718, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138875" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000909", "name": "CD8-positive, alpha-beta memory T cell" }, "cellTypeAuthorAnnotation": "CD8_TRM/EM, Immune", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 29.138084, "sdRefIntergenicDistribution": 1.468059, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 36530, "distinctRankCount": 1240, "maxRank": 20724.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 417307518, "mappedReadsCount": 235248718, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138875" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000192", "name": "smooth muscle cell" }, "cellTypeAuthorAnnotation": "Muscle_smooth_pulmonary, Stroma", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 9.661957, "sdRefIntergenicDistribution": 1.467865, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 117036, "distinctRankCount": 2608, "maxRank": 22589.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 417307518, "mappedReadsCount": 235248718, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138875" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000787", "name": "memory B cell" }, "cellTypeAuthorAnnotation": "B_memory, Immune", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 63.051247, "sdRefIntergenicDistribution": 1.398464, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 16892, "distinctRankCount": 907, "maxRank": 19800.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 417307518, "mappedReadsCount": 235248718, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138875" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000990", "name": "conventional dendritic cell" }, "cellTypeAuthorAnnotation": "DC_1, Immune", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 69.244790, "sdRefIntergenicDistribution": 1.406493, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 15461, "distinctRankCount": 1076, "maxRank": 19463.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 417307518, "mappedReadsCount": 235248718, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138875" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000990", "name": "conventional dendritic cell" }, "cellTypeAuthorAnnotation": "DC_2, Immune", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 24.376448, "sdRefIntergenicDistribution": 1.419880, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 44148, "distinctRankCount": 1902, "maxRank": 21195.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 417307518, "mappedReadsCount": 235248718, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138875" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000990", "name": "conventional dendritic cell" }, "cellTypeAuthorAnnotation": "DC_activated, Immune", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 2432.307315, "sdRefIntergenicDistribution": 1.203521, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 403, "distinctRankCount": 25, "maxRank": 17706.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 417307518, "mappedReadsCount": 235248718, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138875" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000235", "name": "macrophage" }, "cellTypeAuthorAnnotation": "Macro_AW_CX3CR1, Immune", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 11.009106, "sdRefIntergenicDistribution": 1.529765, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 104445, "distinctRankCount": 2544, "maxRank": 22590.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 417307518, "mappedReadsCount": 235248718, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138875" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0002553", "name": "fibroblast of lung" }, "cellTypeAuthorAnnotation": "Fibro_adventitial, Stroma", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 1.445952, "sdRefIntergenicDistribution": 2.292443, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1589849, "distinctRankCount": 5306, "maxRank": 26958.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 417307518, "mappedReadsCount": 235248718, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138875" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0002553", "name": "fibroblast of lung" }, "cellTypeAuthorAnnotation": "Fibro_alveolar, Stroma", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 3.500091, "sdRefIntergenicDistribution": 1.797116, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 402439, "distinctRankCount": 3910, "maxRank": 25325.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 417307518, "mappedReadsCount": 235248718, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138875" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0002553", "name": "fibroblast of lung" }, "cellTypeAuthorAnnotation": "Fibro_peribronchial, Stroma", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 4.319498, "sdRefIntergenicDistribution": 1.773798, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 319293, "distinctRankCount": 3754, "maxRank": 24974.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 417307518, "mappedReadsCount": 235248718, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138875" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0002553", "name": "fibroblast of lung" }, "cellTypeAuthorAnnotation": "Fibro_perichondrial, Stroma", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 4.688399, "sdRefIntergenicDistribution": 1.744876, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 284042, "distinctRankCount": 3389, "maxRank": 24437.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 417307518, "mappedReadsCount": 235248718, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138875" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000913", "name": "effector memory CD8-positive, alpha-beta T cell" }, "cellTypeAuthorAnnotation": "CD8_EM, Immune", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 15.508615, "sdRefIntergenicDistribution": 1.549097, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 72601, "distinctRankCount": 1839, "maxRank": 21789.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 417307518, "mappedReadsCount": 235248718, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138875" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000913", "name": "effector memory CD8-positive, alpha-beta T cell" }, "cellTypeAuthorAnnotation": "CD8_EM/EMRA, Immune", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 16.531282, "sdRefIntergenicDistribution": 1.520386, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 67395, "distinctRankCount": 1829, "maxRank": 21921.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 417307518, "mappedReadsCount": 235248718, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138875" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000097", "name": "mast cell" }, "cellTypeAuthorAnnotation": "Mast_cell , Immune", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 12.847047, "sdRefIntergenicDistribution": 1.651718, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 90154, "distinctRankCount": 2218, "maxRank": 22412.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 417307518, "mappedReadsCount": 235248718, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138875" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000669", "name": "pericyte cell" }, "cellTypeAuthorAnnotation": "Muscle_pericyte_systemic, Stroma", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 22.473647, "sdRefIntergenicDistribution": 1.431267, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 48462, "distinctRankCount": 1682, "maxRank": 21282.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 417307518, "mappedReadsCount": 235248718, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138875" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0001065", "name": "innate lymphoid cell" }, "cellTypeAuthorAnnotation": "ILC, Immune", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 127.404611, "sdRefIntergenicDistribution": 1.285188, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 7993, "distinctRankCount": 478, "maxRank": 18976.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 417307518, "mappedReadsCount": 235248718, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138875" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000897", "name": "CD4-positive, alpha-beta memory T cell" }, "cellTypeAuthorAnnotation": "CD4_TRM, Immune", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 78.249418, "sdRefIntergenicDistribution": 1.384175, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 13150, "distinctRankCount": 638, "maxRank": 19598.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 417307518, "mappedReadsCount": 235248718, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138875" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:1001603", "name": "lung macrophage" }, "cellTypeAuthorAnnotation": "Macro_CCL, Immune", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 251.122788, "sdRefIntergenicDistribution": 1.422264, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 4210, "distinctRankCount": 231, "maxRank": 18308.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 417307518, "mappedReadsCount": 235248718, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138875" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:1001603", "name": "lung macrophage" }, "cellTypeAuthorAnnotation": "Macro_CHIT1, Immune", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 38.344652, "sdRefIntergenicDistribution": 1.363638, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 27328, "distinctRankCount": 1427, "maxRank": 20725.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 417307518, "mappedReadsCount": 235248718, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138875" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:1001603", "name": "lung macrophage" }, "cellTypeAuthorAnnotation": "Macro_intermediate, Immune", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 70.734681, "sdRefIntergenicDistribution": 1.216167, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 14115, "distinctRankCount": 719, "maxRank": 19607.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 417307518, "mappedReadsCount": 235248718, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138875" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:1001603", "name": "lung macrophage" }, "cellTypeAuthorAnnotation": "Macro_interstitial, Immune", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 256.561251, "sdRefIntergenicDistribution": 1.199934, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 3871, "distinctRankCount": 313, "maxRank": 18371.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 417307518, "mappedReadsCount": 235248718, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138875" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:1001603", "name": "lung macrophage" }, "cellTypeAuthorAnnotation": "Macro_intravascular, Immune", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 5.976093, "sdRefIntergenicDistribution": 1.702049, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 215102, "distinctRankCount": 3201, "maxRank": 23849.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 417307518, "mappedReadsCount": 235248718, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138875" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0019018", "name": "blood vessel smooth muscle cell" }, "cellTypeAuthorAnnotation": "Muscle_perivascular_immune_recruiting, Stroma", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 15.797986, "sdRefIntergenicDistribution": 1.419223, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 68577, "distinctRankCount": 1907, "maxRank": 21751.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 417307518, "mappedReadsCount": 235248718, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138875" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0019018", "name": "blood vessel smooth muscle cell" }, "cellTypeAuthorAnnotation": "Muscle_smooth_arterial_systemic, Stroma", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 24.083587, "sdRefIntergenicDistribution": 1.377264, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 44217, "distinctRankCount": 1545, "maxRank": 21159.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 417307518, "mappedReadsCount": 235248718, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138875" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0002368", "name": "respiratory epithelial cell" }, "cellTypeAuthorAnnotation": "Suprabasal, Epithelia", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 3.770755, "sdRefIntergenicDistribution": 1.852399, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 383009, "distinctRankCount": 4106, "maxRank": 24969.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 417307518, "mappedReadsCount": 235248718, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138875" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000186", "name": "myofibroblast cell" }, "cellTypeAuthorAnnotation": "Fibro_myofibroblast, Stroma", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 8.919714, "sdRefIntergenicDistribution": 1.590326, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 133698, "distinctRankCount": 2809, "maxRank": 23225.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 417307518, "mappedReadsCount": 235248718, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138875" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0002633", "name": "respiratory basal cell" }, "cellTypeAuthorAnnotation": "Basal, Epithelia", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 1.629868, "sdRefIntergenicDistribution": 2.363695, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1418277, "distinctRankCount": 5677, "maxRank": 26940.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 417307518, "mappedReadsCount": 235248718, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138875" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0002633", "name": "respiratory basal cell" }, "cellTypeAuthorAnnotation": "Dividing_Basal, Epithelia", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 29.035159, "sdRefIntergenicDistribution": 1.436051, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 37435, "distinctRankCount": 1909, "maxRank": 20998.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 417307518, "mappedReadsCount": 235248718, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138875" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0002633", "name": "respiratory basal cell" }, "cellTypeAuthorAnnotation": "SMG_Basal, Epithelia", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 12.082274, "sdRefIntergenicDistribution": 1.510839, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 94583, "distinctRankCount": 2528, "maxRank": 22774.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 417307518, "mappedReadsCount": 235248718, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138875" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000788", "name": "naive B cell" }, "cellTypeAuthorAnnotation": "B_naive, Immune", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 159.091576, "sdRefIntergenicDistribution": 1.315966, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 6369, "distinctRankCount": 371, "maxRank": 18734.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 417307518, "mappedReadsCount": 235248718, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138875" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000815", "name": "regulatory T cell" }, "cellTypeAuthorAnnotation": "T_reg, Immune", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 26.505033, "sdRefIntergenicDistribution": 1.435450, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 40060, "distinctRankCount": 1464, "maxRank": 20989.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 417307518, "mappedReadsCount": 235248718, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138875" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0009115", "name": "lymph node lymphatic vessel endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_Lymphatic, Vascular", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 12.240074, "sdRefIntergenicDistribution": 1.541608, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 93766, "distinctRankCount": 2343, "maxRank": 22447.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 417307518, "mappedReadsCount": 235248718, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138875" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000985", "name": "IgG plasma cell" }, "cellTypeAuthorAnnotation": "B_plasma_IgG, Immune", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 54.412304, "sdRefIntergenicDistribution": 1.493967, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 19997, "distinctRankCount": 1140, "maxRank": 19992.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 417307518, "mappedReadsCount": 235248718, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138875" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0002543", "name": "vein endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_venous_systemic, Vascular", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 12.615667, "sdRefIntergenicDistribution": 1.533875, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 91026, "distinctRankCount": 2272, "maxRank": 22140.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 417307518, "mappedReadsCount": 235248718, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138875" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0002376", "name": "non-myelinating Schwann cell" }, "cellTypeAuthorAnnotation": "Schwann_nonmyelinating, Stroma", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 21.356577, "sdRefIntergenicDistribution": 1.433844, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 50817, "distinctRankCount": 1866, "maxRank": 21591.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 417307518, "mappedReadsCount": 235248718, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138875" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000146", "name": "simple columnar epithelial cell" }, "cellTypeAuthorAnnotation": "SMG_Duct, Epithelia", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 3.422801, "sdRefIntergenicDistribution": 1.770836, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 406229, "distinctRankCount": 3977, "maxRank": 25055.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 417307518, "mappedReadsCount": 235248718, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138875" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000057", "name": "fibroblast" }, "cellTypeAuthorAnnotation": "NAF_endoneurial, Stroma", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 33.706673, "sdRefIntergenicDistribution": 1.364673, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 31083, "distinctRankCount": 1587, "maxRank": 20619.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 417307518, "mappedReadsCount": 235248718, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138875" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000057", "name": "fibroblast" }, "cellTypeAuthorAnnotation": "NAF_perineurial, Stroma", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 11.776287, "sdRefIntergenicDistribution": 1.510411, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 95449, "distinctRankCount": 2279, "maxRank": 22363.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 417307518, "mappedReadsCount": 235248718, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138875" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000158", "name": "club cell" }, "cellTypeAuthorAnnotation": "Secretory_Club, Epithelia", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 27.715580, "sdRefIntergenicDistribution": 1.416464, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 38820, "distinctRankCount": 1719, "maxRank": 21099.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 417307518, "mappedReadsCount": 235248718, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138875" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000067", "name": "ciliated epithelial cell" }, "cellTypeAuthorAnnotation": "Ciliated, Epithelia", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 53.774718, "sdRefIntergenicDistribution": 1.477349, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 20262, "distinctRankCount": 1256, "maxRank": 20201.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 417307518, "mappedReadsCount": 235248718, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138875" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0001054", "name": "CD14-positive monocyte" }, "cellTypeAuthorAnnotation": "Monocyte_CD14, Immune", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 68.548553, "sdRefIntergenicDistribution": 1.290797, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 14903, "distinctRankCount": 860, "maxRank": 19709.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 417307518, "mappedReadsCount": 235248718, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138875" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000987", "name": "IgA plasma cell" }, "cellTypeAuthorAnnotation": "B_plasma_IgA, Immune", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 23.145326, "sdRefIntergenicDistribution": 1.603113, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 49535, "distinctRankCount": 1756, "maxRank": 21205.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 417307518, "mappedReadsCount": 235248718, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138875" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000160", "name": "goblet cell" }, "cellTypeAuthorAnnotation": "Secretory_Goblet, Epithelia", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 15.315834, "sdRefIntergenicDistribution": 1.507973, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 74386, "distinctRankCount": 2491, "maxRank": 21915.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 417307518, "mappedReadsCount": 235248718, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138875" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000814", "name": "mature NK T cell" }, "cellTypeAuthorAnnotation": "NKT, Immune", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 266.253675, "sdRefIntergenicDistribution": 1.287932, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 3774, "distinctRankCount": 221, "maxRank": 18443.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 417307518, "mappedReadsCount": 235248718, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138875" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0002144", "name": "capillary endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_Cap_g, Vascular", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 61.452297, "sdRefIntergenicDistribution": 1.275172, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 16591, "distinctRankCount": 951, "maxRank": 19653.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 417307518, "mappedReadsCount": 235248718, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138875" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000583", "name": "alveolar macrophage" }, "cellTypeAuthorAnnotation": "Macro_alveolar, Immune", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 143.930974, "sdRefIntergenicDistribution": 1.401505, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 7303, "distinctRankCount": 420, "maxRank": 18878.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 417307518, "mappedReadsCount": 235248718, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138875" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000623", "name": "natural killer cell" }, "cellTypeAuthorAnnotation": "NK_CD11d, Immune", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 507.103123, "sdRefIntergenicDistribution": 1.277629, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1994, "distinctRankCount": 96, "maxRank": 18087.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 417307518, "mappedReadsCount": 235248718, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138875" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000623", "name": "natural killer cell" }, "cellTypeAuthorAnnotation": "NK_CD16hi, Immune", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 134.325051, "sdRefIntergenicDistribution": 1.351306, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 7467, "distinctRankCount": 535, "maxRank": 18961.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 417307518, "mappedReadsCount": 235248718, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138875" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000623", "name": "natural killer cell" }, "cellTypeAuthorAnnotation": "NK_CD56bright, Immune", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 775.754306, "sdRefIntergenicDistribution": 1.208521, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1287, "distinctRankCount": 78, "maxRank": 17888.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 417307518, "mappedReadsCount": 235248718, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138875" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000940", "name": "mucosal invariant T cell" }, "cellTypeAuthorAnnotation": "MAIT, Immune", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 185.819796, "sdRefIntergenicDistribution": 1.397385, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 5499, "distinctRankCount": 357, "maxRank": 18589.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 417307518, "mappedReadsCount": 235248718, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138875" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000980", "name": "plasmablast" }, "cellTypeAuthorAnnotation": "B_plasmablast, Immune", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 122.995046, "sdRefIntergenicDistribution": 1.606501, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 9193, "distinctRankCount": 603, "maxRank": 18938.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 417307518, "mappedReadsCount": 235248718, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138875" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0002396", "name": "CD14-low, CD16-positive monocyte" }, "cellTypeAuthorAnnotation": "Monocyte_CD16, Immune", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 107.900513, "sdRefIntergenicDistribution": 1.300077, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 9395, "distinctRankCount": 606, "maxRank": 19231.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 417307518, "mappedReadsCount": 235248718, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138875" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0019001", "name": "tracheobronchial serous cell" }, "cellTypeAuthorAnnotation": "SMG_Serous, Epithelia", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 1.478303, "sdRefIntergenicDistribution": 2.231363, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1422204, "distinctRankCount": 5508, "maxRank": 26539.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 417307518, "mappedReadsCount": 235248718, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138875" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:1000413", "name": "endothelial cell of artery" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_arterial_systemic, Vascular", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 270.288488, "sdRefIntergenicDistribution": 1.322233, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 3792, "distinctRankCount": 268, "maxRank": 18344.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 417307518, "mappedReadsCount": 235248718, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138875" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000165", "name": "neuroendocrine cell" }, "cellTypeAuthorAnnotation": "Neuroendocrine, Epithelia", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 162.823549, "sdRefIntergenicDistribution": 1.233562, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 5980, "distinctRankCount": 571, "maxRank": 18823.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 417307518, "mappedReadsCount": 235248718, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138875" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0009089", "name": "lung pericyte" }, "cellTypeAuthorAnnotation": "Muscle_pericyte_pulmonary, Stroma", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 786.605496, "sdRefIntergenicDistribution": 1.134907, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1217, "distinctRankCount": 70, "maxRank": 17899.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 417307518, "mappedReadsCount": 235248718, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138875" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000798", "name": "gamma-delta T cell" }, "cellTypeAuthorAnnotation": "gdT, Immune", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 969.404655, "sdRefIntergenicDistribution": 1.319667, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1073, "distinctRankCount": 55, "maxRank": 17872.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 417307518, "mappedReadsCount": 235248718, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138875" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0017000", "name": "pulmonary ionocyte" }, "cellTypeAuthorAnnotation": "Ionocyte_n_Brush, Epithelia", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 137.918514, "sdRefIntergenicDistribution": 1.314869, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 7525, "distinctRankCount": 696, "maxRank": 18934.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 417307518, "mappedReadsCount": 235248718, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138875" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:1001568", "name": "pulmonary artery endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_arterial_pulmonary, Vascular", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 1258.107462, "sdRefIntergenicDistribution": 1.000831, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 768, "distinctRankCount": 36, "maxRank": 17798.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 417307518, "mappedReadsCount": 235248718, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138875" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000218", "name": "myelinating Schwann cell" }, "cellTypeAuthorAnnotation": "Schwann_Myelinating, Stroma", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 383.473186, "sdRefIntergenicDistribution": 1.246960, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 2653, "distinctRankCount": 152, "maxRank": 18272.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 902851548, "mappedReadsCount": 532516601, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138876" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002144", "name": "capillary endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_Cap_a, Vascular", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 22.597774, "sdRefIntergenicDistribution": 1.399392, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 46523, "distinctRankCount": 1535, "maxRank": 21665.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 902851548, "mappedReadsCount": 532516601, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138876" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002144", "name": "capillary endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_Cap_g, Vascular", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 9.802706, "sdRefIntergenicDistribution": 1.556325, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 116775, "distinctRankCount": 2249, "maxRank": 23363.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 902851548, "mappedReadsCount": 532516601, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138876" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000067", "name": "ciliated epithelial cell" }, "cellTypeAuthorAnnotation": "Ciliated, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 12.731464, "sdRefIntergenicDistribution": 1.738042, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 95362, "distinctRankCount": 2447, "maxRank": 22933.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 902851548, "mappedReadsCount": 532516601, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138876" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002396", "name": "CD14-low, CD16-positive monocyte" }, "cellTypeAuthorAnnotation": "Monocyte_CD16, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 17.376575, "sdRefIntergenicDistribution": 1.409964, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 60530, "distinctRankCount": 1667, "maxRank": 21791.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 902851548, "mappedReadsCount": 532516601, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138876" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000909", "name": "CD8-positive, alpha-beta memory T cell" }, "cellTypeAuthorAnnotation": "CD8_TRM, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 5.633708, "sdRefIntergenicDistribution": 1.676149, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 221788, "distinctRankCount": 2800, "maxRank": 24331.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 902851548, "mappedReadsCount": 532516601, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138876" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000909", "name": "CD8-positive, alpha-beta memory T cell" }, "cellTypeAuthorAnnotation": "CD8_TRM/EM, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 20.471557, "sdRefIntergenicDistribution": 1.425699, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 51574, "distinctRankCount": 1484, "maxRank": 21629.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 902851548, "mappedReadsCount": 532516601, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138876" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000897", "name": "CD4-positive, alpha-beta memory T cell" }, "cellTypeAuthorAnnotation": "CD4_TRM, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 48.366407, "sdRefIntergenicDistribution": 1.329426, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 20967, "distinctRankCount": 903, "maxRank": 20374.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 902851548, "mappedReadsCount": 532516601, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138876" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000146", "name": "simple columnar epithelial cell" }, "cellTypeAuthorAnnotation": "SMG_Duct, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 14.094655, "sdRefIntergenicDistribution": 1.391972, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 75535, "distinctRankCount": 1982, "maxRank": 22051.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 902851548, "mappedReadsCount": 532516601, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138876" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000097", "name": "mast cell" }, "cellTypeAuthorAnnotation": "Mast_cell , Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 19.550812, "sdRefIntergenicDistribution": 1.463623, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 54111, "distinctRankCount": 1549, "maxRank": 21692.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 902851548, "mappedReadsCount": 532516601, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138876" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002633", "name": "respiratory basal cell" }, "cellTypeAuthorAnnotation": "Basal, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 12.589934, "sdRefIntergenicDistribution": 1.411494, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 87111, "distinctRankCount": 2019, "maxRank": 22467.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 902851548, "mappedReadsCount": 532516601, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138876" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002633", "name": "respiratory basal cell" }, "cellTypeAuthorAnnotation": "Dividing_Basal, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 1186.935212, "sdRefIntergenicDistribution": 1.231821, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 769, "distinctRankCount": 12, "maxRank": 17835.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 902851548, "mappedReadsCount": 532516601, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138876" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002633", "name": "respiratory basal cell" }, "cellTypeAuthorAnnotation": "SMG_Basal, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 344.330225, "sdRefIntergenicDistribution": 1.181328, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 2829, "distinctRankCount": 88, "maxRank": 18109.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 902851548, "mappedReadsCount": 532516601, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138876" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000624", "name": "CD4-positive, alpha-beta T cell" }, "cellTypeAuthorAnnotation": "CD4_EM/Effector, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 4.909274, "sdRefIntergenicDistribution": 1.701811, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 258920, "distinctRankCount": 2823, "maxRank": 24803.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 902851548, "mappedReadsCount": 532516601, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138876" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000624", "name": "CD4-positive, alpha-beta T cell" }, "cellTypeAuthorAnnotation": "CD4_naive/CM, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 5.102937, "sdRefIntergenicDistribution": 1.700214, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 248545, "distinctRankCount": 2903, "maxRank": 24566.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 902851548, "mappedReadsCount": 532516601, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138876" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000583", "name": "alveolar macrophage" }, "cellTypeAuthorAnnotation": "Macro_alveolar, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 9.140483, "sdRefIntergenicDistribution": 1.596928, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 128354, "distinctRankCount": 2503, "maxRank": 23309.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 902851548, "mappedReadsCount": 532516601, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138876" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000815", "name": "regulatory T cell" }, "cellTypeAuthorAnnotation": "T_reg, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 22.514972, "sdRefIntergenicDistribution": 1.397052, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 46614, "distinctRankCount": 1490, "maxRank": 21731.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 902851548, "mappedReadsCount": 532516601, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138876" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002553", "name": "fibroblast of lung" }, "cellTypeAuthorAnnotation": "Fibro_adventitial, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 2.435255, "sdRefIntergenicDistribution": 1.892013, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 628163, "distinctRankCount": 3971, "maxRank": 26073.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 902851548, "mappedReadsCount": 532516601, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138876" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002553", "name": "fibroblast of lung" }, "cellTypeAuthorAnnotation": "Fibro_alveolar, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 2.062736, "sdRefIntergenicDistribution": 2.157742, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 910915, "distinctRankCount": 4646, "maxRank": 26567.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 902851548, "mappedReadsCount": 532516601, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138876" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002553", "name": "fibroblast of lung" }, "cellTypeAuthorAnnotation": "Fibro_peribronchial, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 15.715414, "sdRefIntergenicDistribution": 1.372078, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 67202, "distinctRankCount": 1915, "maxRank": 22310.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 902851548, "mappedReadsCount": 532516601, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138876" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002553", "name": "fibroblast of lung" }, "cellTypeAuthorAnnotation": "Fibro_perichondrial, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 296.755944, "sdRefIntergenicDistribution": 1.251571, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 3377, "distinctRankCount": 171, "maxRank": 18280.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 902851548, "mappedReadsCount": 532516601, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138876" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002553", "name": "fibroblast of lung" }, "cellTypeAuthorAnnotation": "Fibro_perichondrial, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 27.880011, "sdRefIntergenicDistribution": 1.335483, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 37689, "distinctRankCount": 1394, "maxRank": 20706.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 902851548, "mappedReadsCount": 532516601, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138876" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:1001603", "name": "lung macrophage" }, "cellTypeAuthorAnnotation": "Macro_CCL, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 550.067003, "sdRefIntergenicDistribution": 1.250607, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1781, "distinctRankCount": 71, "maxRank": 18049.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 902851548, "mappedReadsCount": 532516601, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138876" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:1001603", "name": "lung macrophage" }, "cellTypeAuthorAnnotation": "Macro_CHIT1, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 19.086120, "sdRefIntergenicDistribution": 1.483237, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 56786, "distinctRankCount": 2048, "maxRank": 21557.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 902851548, "mappedReadsCount": 532516601, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138876" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:1001603", "name": "lung macrophage" }, "cellTypeAuthorAnnotation": "Macro_intermediate, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 95.467061, "sdRefIntergenicDistribution": 1.232816, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 10217, "distinctRankCount": 518, "maxRank": 19333.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 902851548, "mappedReadsCount": 532516601, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138876" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:1001603", "name": "lung macrophage" }, "cellTypeAuthorAnnotation": "Macro_interstitial, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 105.299232, "sdRefIntergenicDistribution": 1.251551, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 9456, "distinctRankCount": 599, "maxRank": 19076.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 902851548, "mappedReadsCount": 532516601, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138876" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:1001603", "name": "lung macrophage" }, "cellTypeAuthorAnnotation": "Macro_intravascular, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 15.954400, "sdRefIntergenicDistribution": 1.487939, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 69168, "distinctRankCount": 1826, "maxRank": 22074.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 902851548, "mappedReadsCount": 532516601, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138876" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000623", "name": "natural killer cell" }, "cellTypeAuthorAnnotation": "NK_CD11d, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 74.157476, "sdRefIntergenicDistribution": 1.285611, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 13324, "distinctRankCount": 628, "maxRank": 19773.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 902851548, "mappedReadsCount": 532516601, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138876" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000623", "name": "natural killer cell" }, "cellTypeAuthorAnnotation": "NK_CD16hi, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 11.411019, "sdRefIntergenicDistribution": 1.478367, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 95470, "distinctRankCount": 1927, "maxRank": 23089.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 902851548, "mappedReadsCount": 532516601, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138876" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000623", "name": "natural killer cell" }, "cellTypeAuthorAnnotation": "NK_CD56bright, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 80.659956, "sdRefIntergenicDistribution": 1.286454, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 12535, "distinctRankCount": 676, "maxRank": 19612.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 902851548, "mappedReadsCount": 532516601, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138876" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000985", "name": "IgG plasma cell" }, "cellTypeAuthorAnnotation": "B_plasma_IgG, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 12.994684, "sdRefIntergenicDistribution": 1.649513, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 88648, "distinctRankCount": 2112, "maxRank": 22449.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 902851548, "mappedReadsCount": 532516601, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138876" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0009115", "name": "lymph node lymphatic vessel endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_Lymphatic, Vascular", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 9.325296, "sdRefIntergenicDistribution": 1.517082, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 120361, "distinctRankCount": 2417, "maxRank": 23513.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 902851548, "mappedReadsCount": 532516601, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138876" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000913", "name": "effector memory CD8-positive, alpha-beta T cell" }, "cellTypeAuthorAnnotation": "CD8_EM, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 14.696433, "sdRefIntergenicDistribution": 1.402958, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 71990, "distinctRankCount": 1713, "maxRank": 22215.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 902851548, "mappedReadsCount": 532516601, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138876" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000913", "name": "effector memory CD8-positive, alpha-beta T cell" }, "cellTypeAuthorAnnotation": "CD8_EM/EMRA, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 41.474275, "sdRefIntergenicDistribution": 1.342591, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 24638, "distinctRankCount": 1038, "maxRank": 20568.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 902851548, "mappedReadsCount": 532516601, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138876" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000186", "name": "myofibroblast cell" }, "cellTypeAuthorAnnotation": "Fibro_myofibroblast, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 50.438544, "sdRefIntergenicDistribution": 1.293765, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 20029, "distinctRankCount": 953, "maxRank": 20352.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 902851548, "mappedReadsCount": 532516601, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138876" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000158", "name": "club cell" }, "cellTypeAuthorAnnotation": "Secretory_Club, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 5.053667, "sdRefIntergenicDistribution": 1.684905, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 247908, "distinctRankCount": 3101, "maxRank": 24386.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 902851548, "mappedReadsCount": 532516601, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138876" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0001065", "name": "innate lymphoid cell" }, "cellTypeAuthorAnnotation": "ILC, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 145.785241, "sdRefIntergenicDistribution": 1.193277, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 6466, "distinctRankCount": 337, "maxRank": 18932.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 902851548, "mappedReadsCount": 532516601, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138876" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000192", "name": "smooth muscle cell" }, "cellTypeAuthorAnnotation": "Muscle_smooth_pulmonary, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 11.539970, "sdRefIntergenicDistribution": 1.437806, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 95104, "distinctRankCount": 2174, "maxRank": 22721.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 902851548, "mappedReadsCount": 532516601, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138876" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0019001", "name": "tracheobronchial serous cell" }, "cellTypeAuthorAnnotation": "SMG_Serous, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 1.653847, "sdRefIntergenicDistribution": 2.077542, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1104529, "distinctRankCount": 4731, "maxRank": 26248.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 902851548, "mappedReadsCount": 532516601, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138876" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0019019", "name": "tracheobronchial smooth muscle cell" }, "cellTypeAuthorAnnotation": "Muscle_smooth_airway, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 50.799357, "sdRefIntergenicDistribution": 1.227341, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 19673, "distinctRankCount": 998, "maxRank": 19846.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 902851548, "mappedReadsCount": 532516601, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138876" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000990", "name": "conventional dendritic cell" }, "cellTypeAuthorAnnotation": "DC_1, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 132.242048, "sdRefIntergenicDistribution": 1.217750, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 7330, "distinctRankCount": 457, "maxRank": 18963.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 902851548, "mappedReadsCount": 532516601, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138876" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000990", "name": "conventional dendritic cell" }, "cellTypeAuthorAnnotation": "DC_2, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 38.718960, "sdRefIntergenicDistribution": 1.340851, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 26237, "distinctRankCount": 1167, "maxRank": 20739.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 902851548, "mappedReadsCount": 532516601, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138876" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0019018", "name": "blood vessel smooth muscle cell" }, "cellTypeAuthorAnnotation": "Muscle_perivascular_immune_recruiting, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 76.605772, "sdRefIntergenicDistribution": 1.234295, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 12911, "distinctRankCount": 665, "maxRank": 19393.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 902851548, "mappedReadsCount": 532516601, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138876" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0019018", "name": "blood vessel smooth muscle cell" }, "cellTypeAuthorAnnotation": "Muscle_smooth_arterial_systemic, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 58.034139, "sdRefIntergenicDistribution": 1.280843, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 17739, "distinctRankCount": 740, "maxRank": 19618.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 902851548, "mappedReadsCount": 532516601, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138876" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0001054", "name": "CD14-positive monocyte" }, "cellTypeAuthorAnnotation": "Monocyte_CD14, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 23.691193, "sdRefIntergenicDistribution": 1.379294, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 43400, "distinctRankCount": 1517, "maxRank": 21477.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 902851548, "mappedReadsCount": 532516601, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138876" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002063", "name": "type II pneumocyte" }, "cellTypeAuthorAnnotation": "AT2, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 0.950500, "sdRefIntergenicDistribution": 2.883039, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 4540724, "distinctRankCount": 6705, "maxRank": 27904.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 902851548, "mappedReadsCount": 532516601, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138876" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002063", "name": "type II pneumocyte" }, "cellTypeAuthorAnnotation": "Dividing_AT2, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 33.654713, "sdRefIntergenicDistribution": 1.379897, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 29827, "distinctRankCount": 1483, "maxRank": 20931.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 902851548, "mappedReadsCount": 532516601, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138876" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002543", "name": "vein endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_venous_pulmonary, Vascular", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 32.654687, "sdRefIntergenicDistribution": 1.394603, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 32376, "distinctRankCount": 1312, "maxRank": 21039.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 902851548, "mappedReadsCount": 532516601, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138876" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002543", "name": "vein endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_venous_systemic, Vascular", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 22.899425, "sdRefIntergenicDistribution": 1.361904, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 45408, "distinctRankCount": 1638, "maxRank": 21319.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 902851548, "mappedReadsCount": 532516601, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138876" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0009089", "name": "lung pericyte" }, "cellTypeAuthorAnnotation": "Muscle_pericyte_pulmonary, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 33.375635, "sdRefIntergenicDistribution": 1.376872, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 31130, "distinctRankCount": 1223, "maxRank": 20874.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 902851548, "mappedReadsCount": 532516601, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138876" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000814", "name": "mature NK T cell" }, "cellTypeAuthorAnnotation": "NKT, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 78.213034, "sdRefIntergenicDistribution": 1.234045, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 12490, "distinctRankCount": 571, "maxRank": 19660.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 902851548, "mappedReadsCount": 532516601, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138876" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000160", "name": "goblet cell" }, "cellTypeAuthorAnnotation": "Secretory_Goblet, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 36.185349, "sdRefIntergenicDistribution": 1.344457, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 29000, "distinctRankCount": 1339, "maxRank": 20458.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 902851548, "mappedReadsCount": 532516601, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138876" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000940", "name": "mucosal invariant T cell" }, "cellTypeAuthorAnnotation": "MAIT, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 45.100474, "sdRefIntergenicDistribution": 1.327163, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 22508, "distinctRankCount": 974, "maxRank": 20290.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 902851548, "mappedReadsCount": 532516601, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138876" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000319", "name": "mucus secreting cell" }, "cellTypeAuthorAnnotation": "SMG_Mucous, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 1.602777, "sdRefIntergenicDistribution": 2.064121, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1112999, "distinctRankCount": 4662, "maxRank": 25873.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 902851548, "mappedReadsCount": 532516601, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138876" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:1001568", "name": "pulmonary artery endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_arterial_pulmonary, Vascular", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 44.496755, "sdRefIntergenicDistribution": 1.337603, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 22714, "distinctRankCount": 1026, "maxRank": 20370.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 902851548, "mappedReadsCount": 532516601, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138876" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000185", "name": "myoepithelial cell" }, "cellTypeAuthorAnnotation": "Myoepithelial, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 16.629803, "sdRefIntergenicDistribution": 1.434214, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 65062, "distinctRankCount": 1900, "maxRank": 21577.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 902851548, "mappedReadsCount": 532516601, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138876" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000798", "name": "gamma-delta T cell" }, "cellTypeAuthorAnnotation": "gdT, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 53.459223, "sdRefIntergenicDistribution": 1.281558, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 18833, "distinctRankCount": 834, "maxRank": 20239.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 902851548, "mappedReadsCount": 532516601, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138876" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000788", "name": "naive B cell" }, "cellTypeAuthorAnnotation": "B_naive, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 49.990589, "sdRefIntergenicDistribution": 1.373637, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 20350, "distinctRankCount": 900, "maxRank": 20325.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 902851548, "mappedReadsCount": 532516601, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138876" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000235", "name": "macrophage" }, "cellTypeAuthorAnnotation": "Macro_AW_CX3CR1, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 31.536422, "sdRefIntergenicDistribution": 1.342604, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 33126, "distinctRankCount": 1291, "maxRank": 20681.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 902851548, "mappedReadsCount": 532516601, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138876" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000987", "name": "IgA plasma cell" }, "cellTypeAuthorAnnotation": "B_plasma_IgA, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 23.505661, "sdRefIntergenicDistribution": 1.513430, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 46184, "distinctRankCount": 1529, "maxRank": 21288.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 902851548, "mappedReadsCount": 532516601, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138876" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000057", "name": "fibroblast" }, "cellTypeAuthorAnnotation": "NAF_endoneurial, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 480.912997, "sdRefIntergenicDistribution": 1.179044, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 2085, "distinctRankCount": 123, "maxRank": 17989.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 902851548, "mappedReadsCount": 532516601, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138876" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000057", "name": "fibroblast" }, "cellTypeAuthorAnnotation": "NAF_perineurial, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 340.497929, "sdRefIntergenicDistribution": 1.136070, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 2847, "distinctRankCount": 96, "maxRank": 18207.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 902851548, "mappedReadsCount": 532516601, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138876" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002376", "name": "non-myelinating Schwann cell" }, "cellTypeAuthorAnnotation": "Schwann_nonmyelinating, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 473.289356, "sdRefIntergenicDistribution": 1.202866, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 2131, "distinctRankCount": 47, "maxRank": 18141.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 902851548, "mappedReadsCount": 532516601, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138876" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000787", "name": "memory B cell" }, "cellTypeAuthorAnnotation": "B_memory, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 21.135655, "sdRefIntergenicDistribution": 1.488305, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 50294, "distinctRankCount": 1554, "maxRank": 21663.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 902851548, "mappedReadsCount": 532516601, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138876" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000138", "name": "chondrocyte" }, "cellTypeAuthorAnnotation": "Chondrocyte, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 100.446154, "sdRefIntergenicDistribution": 1.187570, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 9595, "distinctRankCount": 531, "maxRank": 19303.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 902851548, "mappedReadsCount": 532516601, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138876" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002368", "name": "respiratory epithelial cell" }, "cellTypeAuthorAnnotation": "Suprabasal, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 34.274643, "sdRefIntergenicDistribution": 1.372620, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 31140, "distinctRankCount": 1269, "maxRank": 20344.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 902851548, "mappedReadsCount": 532516601, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138876" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000165", "name": "neuroendocrine cell" }, "cellTypeAuthorAnnotation": "Neuroendocrine, Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 68.847056, "sdRefIntergenicDistribution": 1.366350, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 15384, "distinctRankCount": 976, "maxRank": 19700.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 902851548, "mappedReadsCount": 532516601, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138876" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000077", "name": "mesothelial cell" }, "cellTypeAuthorAnnotation": "Mesothelia, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 34.860882, "sdRefIntergenicDistribution": 1.389327, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 30079, "distinctRankCount": 1316, "maxRank": 20689.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 902851548, "mappedReadsCount": 532516601, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138876" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:1000413", "name": "endothelial cell of artery" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_arterial_systemic, Vascular", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 164.424139, "sdRefIntergenicDistribution": 1.257702, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 5943, "distinctRankCount": 358, "maxRank": 18781.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 902851548, "mappedReadsCount": 532516601, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138876" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000784", "name": "plasmacytoid dendritic cell" }, "cellTypeAuthorAnnotation": "DC_plasmacytoid, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 1698.552955, "sdRefIntergenicDistribution": 1.001550, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 560, "distinctRankCount": 29, "maxRank": 17769.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 902851548, "mappedReadsCount": 532516601, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138876" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0002062", "name": "type I pneumocyte" }, "cellTypeAuthorAnnotation": "AT1 , Epithelia", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 1.692664, "sdRefIntergenicDistribution": 2.324439, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1248983, "distinctRankCount": 4932, "maxRank": 26613.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 902851548, "mappedReadsCount": 532516601, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138876" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000669", "name": "pericyte cell" }, "cellTypeAuthorAnnotation": "Muscle_pericyte_systemic, Stroma", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 368.439719, "sdRefIntergenicDistribution": 1.155274, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 2570, "distinctRankCount": 121, "maxRank": 18182.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 902851548, "mappedReadsCount": 532516601, "minReadLength": 91, "maxReadLength": 151 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138876" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002048", "name": "lung" }, "anatEntityAuthorAnnotation": "Mix", "cellType": { "id": "CL:0000980", "name": "plasmablast" }, "cellTypeAuthorAnnotation": "B_plasmablast, Immune", "devStage": { "id": "UBERON:0000113", "name": "post-juvenile" }, "devStageAuthorAnnotation": "55-64", "sex": "mixed", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 1375.280944, "sdRefIntergenicDistribution": 1.284172, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 729, "distinctRankCount": 21, "maxRank": 17810.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 174727583, "mappedReadsCount": 127449240, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138877" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0002144", "name": "capillary endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_Cap_a, Vascular", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 8.252833, "sdRefIntergenicDistribution": 1.545852, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 144890, "distinctRankCount": 400, "maxRank": 22608.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 174727583, "mappedReadsCount": 127449240, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138877" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0002144", "name": "capillary endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_Cap_g, Vascular", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 6.165460, "sdRefIntergenicDistribution": 1.610049, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 204798, "distinctRankCount": 506, "maxRank": 23051.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 174727583, "mappedReadsCount": 127449240, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138877" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000583", "name": "alveolar macrophage" }, "cellTypeAuthorAnnotation": "Macro_alveolar, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 2.039365, "sdRefIntergenicDistribution": 1.799920, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 709582, "distinctRankCount": 1060, "maxRank": 23629.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 174727583, "mappedReadsCount": 127449240, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138877" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0002062", "name": "type I pneumocyte" }, "cellTypeAuthorAnnotation": "AT1 , Epithelia", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 9.136174, "sdRefIntergenicDistribution": 1.494826, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 128544, "distinctRankCount": 458, "maxRank": 22173.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 174727583, "mappedReadsCount": 127449240, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138877" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000814", "name": "mature NK T cell" }, "cellTypeAuthorAnnotation": "NKT, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 5.498230, "sdRefIntergenicDistribution": 1.728042, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 242107, "distinctRankCount": 501, "maxRank": 22563.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 174727583, "mappedReadsCount": 127449240, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138877" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:1001568", "name": "pulmonary artery endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_arterial_pulmonary, Vascular", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 5.874451, "sdRefIntergenicDistribution": 1.683622, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 218918, "distinctRankCount": 596, "maxRank": 22882.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 174727583, "mappedReadsCount": 127449240, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138877" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0009089", "name": "lung pericyte" }, "cellTypeAuthorAnnotation": "Muscle_pericyte_pulmonary, Stroma", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 11.149933, "sdRefIntergenicDistribution": 1.460416, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 103218, "distinctRankCount": 452, "maxRank": 22019.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 174727583, "mappedReadsCount": 127449240, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138877" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000798", "name": "gamma-delta T cell" }, "cellTypeAuthorAnnotation": "gdT, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 28.635432, "sdRefIntergenicDistribution": 1.496606, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 38312, "distinctRankCount": 216, "maxRank": 20265.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 174727583, "mappedReadsCount": 127449240, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138877" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000990", "name": "conventional dendritic cell" }, "cellTypeAuthorAnnotation": "DC_2, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 11.561383, "sdRefIntergenicDistribution": 1.677515, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 107961, "distinctRankCount": 423, "maxRank": 21351.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 174727583, "mappedReadsCount": 127449240, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138877" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000990", "name": "conventional dendritic cell" }, "cellTypeAuthorAnnotation": "DC_activated, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 139.077794, "sdRefIntergenicDistribution": 1.520617, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 7474, "distinctRankCount": 81, "maxRank": 18524.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 174727583, "mappedReadsCount": 127449240, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138877" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0002543", "name": "vein endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_venous_pulmonary, Vascular", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 3.639020, "sdRefIntergenicDistribution": 1.633770, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 352777, "distinctRankCount": 764, "maxRank": 23240.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 174727583, "mappedReadsCount": 127449240, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138877" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0002543", "name": "vein endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_venous_systemic, Vascular", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 12.727200, "sdRefIntergenicDistribution": 1.554683, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 92797, "distinctRankCount": 386, "maxRank": 21440.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 174727583, "mappedReadsCount": 127449240, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138877" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000624", "name": "CD4-positive, alpha-beta T cell" }, "cellTypeAuthorAnnotation": "CD4_EM/Effector, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 18.772226, "sdRefIntergenicDistribution": 1.582748, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 60176, "distinctRankCount": 270, "maxRank": 21010.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 174727583, "mappedReadsCount": 127449240, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138877" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000624", "name": "CD4-positive, alpha-beta T cell" }, "cellTypeAuthorAnnotation": "CD4_naive/CM, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 28.249992, "sdRefIntergenicDistribution": 1.457885, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 38393, "distinctRankCount": 207, "maxRank": 20014.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 174727583, "mappedReadsCount": 127449240, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138877" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000057", "name": "fibroblast" }, "cellTypeAuthorAnnotation": "NAF_endoneurial, Stroma", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 274.849382, "sdRefIntergenicDistribution": 1.382183, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 3713, "distinctRankCount": 44, "maxRank": 18198.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 174727583, "mappedReadsCount": 127449240, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138877" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0002553", "name": "fibroblast of lung" }, "cellTypeAuthorAnnotation": "Fibro_adventitial, Stroma", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 0.883825, "sdRefIntergenicDistribution": 2.187227, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 2389425, "distinctRankCount": 2448, "maxRank": 25616.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 174727583, "mappedReadsCount": 127449240, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138877" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0002553", "name": "fibroblast of lung" }, "cellTypeAuthorAnnotation": "Fibro_alveolar, Stroma", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 3.037965, "sdRefIntergenicDistribution": 1.695303, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 452778, "distinctRankCount": 792, "maxRank": 23983.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 174727583, "mappedReadsCount": 127449240, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138877" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0002553", "name": "fibroblast of lung" }, "cellTypeAuthorAnnotation": "Fibro_immune_recruiting, Stroma", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 118.113036, "sdRefIntergenicDistribution": 1.185422, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 8453, "distinctRankCount": 70, "maxRank": 18855.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 174727583, "mappedReadsCount": 127449240, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138877" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0002553", "name": "fibroblast of lung" }, "cellTypeAuthorAnnotation": "Fibro_peribronchial, Stroma", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 33.614155, "sdRefIntergenicDistribution": 1.304812, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 31368, "distinctRankCount": 189, "maxRank": 20268.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 174727583, "mappedReadsCount": 127449240, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138877" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000192", "name": "smooth muscle cell" }, "cellTypeAuthorAnnotation": "Muscle_smooth_pulmonary, Stroma", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 3.719449, "sdRefIntergenicDistribution": 1.574923, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 335526, "distinctRankCount": 667, "maxRank": 23288.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 174727583, "mappedReadsCount": 127449240, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138877" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000913", "name": "effector memory CD8-positive, alpha-beta T cell" }, "cellTypeAuthorAnnotation": "CD8_EM, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 36.600000, "sdRefIntergenicDistribution": 1.459710, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 29338, "distinctRankCount": 158, "maxRank": 19691.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 174727583, "mappedReadsCount": 127449240, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138877" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000913", "name": "effector memory CD8-positive, alpha-beta T cell" }, "cellTypeAuthorAnnotation": "CD8_EM/EMRA, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 5.077694, "sdRefIntergenicDistribution": 1.713102, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 262416, "distinctRankCount": 541, "maxRank": 22654.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 174727583, "mappedReadsCount": 127449240, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138877" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0002633", "name": "respiratory basal cell" }, "cellTypeAuthorAnnotation": "Basal, Epithelia", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 59.355265, "sdRefIntergenicDistribution": 1.298810, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 17319, "distinctRankCount": 142, "maxRank": 19487.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 174727583, "mappedReadsCount": 127449240, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138877" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0001054", "name": "CD14-positive monocyte" }, "cellTypeAuthorAnnotation": "Monocyte_CD14, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 13.888578, "sdRefIntergenicDistribution": 1.614678, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 86977, "distinctRankCount": 308, "maxRank": 20757.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 174727583, "mappedReadsCount": 127449240, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138877" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000909", "name": "CD8-positive, alpha-beta memory T cell" }, "cellTypeAuthorAnnotation": "CD8_TRM, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 805.587150, "sdRefIntergenicDistribution": 1.251670, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1145, "distinctRankCount": 21, "maxRank": 17819.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 174727583, "mappedReadsCount": 127449240, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138877" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000909", "name": "CD8-positive, alpha-beta memory T cell" }, "cellTypeAuthorAnnotation": "CD8_TRM/EM, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 15.147455, "sdRefIntergenicDistribution": 1.547957, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 75901, "distinctRankCount": 290, "maxRank": 21112.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 174727583, "mappedReadsCount": 127449240, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138877" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0002396", "name": "CD14-low, CD16-positive monocyte" }, "cellTypeAuthorAnnotation": "Monocyte_CD16, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 79.885488, "sdRefIntergenicDistribution": 1.486890, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 13956, "distinctRankCount": 120, "maxRank": 18818.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 174727583, "mappedReadsCount": 127449240, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138877" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000186", "name": "myofibroblast cell" }, "cellTypeAuthorAnnotation": "Fibro_myofibroblast, Stroma", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 6.339172, "sdRefIntergenicDistribution": 1.540089, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 190076, "distinctRankCount": 526, "maxRank": 22864.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 174727583, "mappedReadsCount": 127449240, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138877" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000623", "name": "natural killer cell" }, "cellTypeAuthorAnnotation": "NK_CD11d, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 118.090319, "sdRefIntergenicDistribution": 1.260920, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 8577, "distinctRankCount": 75, "maxRank": 18682.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 174727583, "mappedReadsCount": 127449240, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138877" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000623", "name": "natural killer cell" }, "cellTypeAuthorAnnotation": "NK_CD16hi, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 9.349348, "sdRefIntergenicDistribution": 1.704289, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 135974, "distinctRankCount": 399, "maxRank": 22159.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 174727583, "mappedReadsCount": 127449240, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138877" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000623", "name": "natural killer cell" }, "cellTypeAuthorAnnotation": "NK_CD56bright, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 11.246789, "sdRefIntergenicDistribution": 1.687311, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 110938, "distinctRankCount": 412, "maxRank": 21784.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 174727583, "mappedReadsCount": 127449240, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138877" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:1001603", "name": "lung macrophage" }, "cellTypeAuthorAnnotation": "Macro_CCL, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 81.471319, "sdRefIntergenicDistribution": 1.520426, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 13079, "distinctRankCount": 102, "maxRank": 18824.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 174727583, "mappedReadsCount": 127449240, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138877" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:1001603", "name": "lung macrophage" }, "cellTypeAuthorAnnotation": "Macro_CHIT1, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 29.560308, "sdRefIntergenicDistribution": 1.468855, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 39780, "distinctRankCount": 209, "maxRank": 19803.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 174727583, "mappedReadsCount": 127449240, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138877" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:1001603", "name": "lung macrophage" }, "cellTypeAuthorAnnotation": "Macro_intermediate, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 16.809635, "sdRefIntergenicDistribution": 1.631274, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 71689, "distinctRankCount": 328, "maxRank": 20904.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 174727583, "mappedReadsCount": 127449240, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138877" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:1001603", "name": "lung macrophage" }, "cellTypeAuthorAnnotation": "Macro_intravascular, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 8.073226, "sdRefIntergenicDistribution": 1.607134, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 151381, "distinctRankCount": 436, "maxRank": 22186.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 174727583, "mappedReadsCount": 127449240, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138877" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000897", "name": "CD4-positive, alpha-beta memory T cell" }, "cellTypeAuthorAnnotation": "CD4_TRM, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 31.692933, "sdRefIntergenicDistribution": 1.499016, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 34105, "distinctRankCount": 189, "maxRank": 20028.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 174727583, "mappedReadsCount": 127449240, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138877" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000077", "name": "mesothelial cell" }, "cellTypeAuthorAnnotation": "Mesothelia, Stroma", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 1279.046434, "sdRefIntergenicDistribution": 1.125985, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 687, "distinctRankCount": 11, "maxRank": 17776.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 174727583, "mappedReadsCount": 127449240, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138877" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000097", "name": "mast cell" }, "cellTypeAuthorAnnotation": "Mast_cell , Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 4.335849, "sdRefIntergenicDistribution": 2.044664, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 365737, "distinctRankCount": 598, "maxRank": 23416.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 174727583, "mappedReadsCount": 127449240, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138877" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:1000413", "name": "endothelial cell of artery" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_arterial_systemic, Vascular", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 188.460924, "sdRefIntergenicDistribution": 1.355353, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 5816, "distinctRankCount": 56, "maxRank": 18483.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 174727583, "mappedReadsCount": 127449240, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138877" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000940", "name": "mucosal invariant T cell" }, "cellTypeAuthorAnnotation": "MAIT, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 17.585669, "sdRefIntergenicDistribution": 1.528520, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 64581, "distinctRankCount": 281, "maxRank": 20748.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 174727583, "mappedReadsCount": 127449240, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138877" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0002063", "name": "type II pneumocyte" }, "cellTypeAuthorAnnotation": "AT2, Epithelia", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 0.894836, "sdRefIntergenicDistribution": 2.572377, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 3759341, "distinctRankCount": 2412, "maxRank": 26010.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 174727583, "mappedReadsCount": 127449240, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138877" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0002063", "name": "type II pneumocyte" }, "cellTypeAuthorAnnotation": "Dividing_AT2, Epithelia", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 34.776608, "sdRefIntergenicDistribution": 1.349281, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 31894, "distinctRankCount": 220, "maxRank": 19810.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 174727583, "mappedReadsCount": 127449240, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138877" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000987", "name": "IgA plasma cell" }, "cellTypeAuthorAnnotation": "B_plasma_IgA, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 29.302691, "sdRefIntergenicDistribution": 1.416476, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 37235, "distinctRankCount": 145, "maxRank": 19297.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 174727583, "mappedReadsCount": 127449240, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138877" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0019018", "name": "blood vessel smooth muscle cell" }, "cellTypeAuthorAnnotation": "Muscle_smooth_arterial_systemic, Stroma", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 61.526900, "sdRefIntergenicDistribution": 1.286964, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 17396, "distinctRankCount": 129, "maxRank": 19234.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 174727583, "mappedReadsCount": 127449240, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138877" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000158", "name": "club cell" }, "cellTypeAuthorAnnotation": "Secretory_Club, Epithelia", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 2.858882, "sdRefIntergenicDistribution": 1.881208, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 552576, "distinctRankCount": 1393, "maxRank": 24195.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 174727583, "mappedReadsCount": 127449240, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138877" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000787", "name": "memory B cell" }, "cellTypeAuthorAnnotation": "B_memory, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 8.980803, "sdRefIntergenicDistribution": 1.574533, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 133480, "distinctRankCount": 389, "maxRank": 21500.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 174727583, "mappedReadsCount": 127449240, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138877" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000067", "name": "ciliated epithelial cell" }, "cellTypeAuthorAnnotation": "Ciliated, Epithelia", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 9.111424, "sdRefIntergenicDistribution": 1.620304, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 136747, "distinctRankCount": 804, "maxRank": 23079.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 174727583, "mappedReadsCount": 127449240, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138877" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0009115", "name": "lymph node lymphatic vessel endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_Lymphatic, Vascular", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 5.146969, "sdRefIntergenicDistribution": 1.605776, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 243195, "distinctRankCount": 615, "maxRank": 23120.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 174727583, "mappedReadsCount": 127449240, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138877" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000985", "name": "IgG plasma cell" }, "cellTypeAuthorAnnotation": "B_plasma_IgG, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 220.297170, "sdRefIntergenicDistribution": 1.283172, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 4605, "distinctRankCount": 39, "maxRank": 18080.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 174727583, "mappedReadsCount": 127449240, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138877" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000160", "name": "goblet cell" }, "cellTypeAuthorAnnotation": "Secretory_Goblet, Epithelia", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 160.032557, "sdRefIntergenicDistribution": 1.336411, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 6608, "distinctRankCount": 65, "maxRank": 18359.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 174727583, "mappedReadsCount": 127449240, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138877" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0019019", "name": "tracheobronchial smooth muscle cell" }, "cellTypeAuthorAnnotation": "Muscle_smooth_airway, Stroma", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 815.660685, "sdRefIntergenicDistribution": 0.000000, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 0, "distinctRankCount": 0 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 174727583, "mappedReadsCount": 127449240, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138877" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000815", "name": "regulatory T cell" }, "cellTypeAuthorAnnotation": "T_reg, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 106.844696, "sdRefIntergenicDistribution": 1.280054, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 9358, "distinctRankCount": 84, "maxRank": 18811.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 174727583, "mappedReadsCount": 127449240, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138877" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0001065", "name": "innate lymphoid cell" }, "cellTypeAuthorAnnotation": "ILC, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 109.675859, "sdRefIntergenicDistribution": 1.337870, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 9547, "distinctRankCount": 83, "maxRank": 18652.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 174727583, "mappedReadsCount": 127449240, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138877" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000788", "name": "naive B cell" }, "cellTypeAuthorAnnotation": "B_naive, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 168.110833, "sdRefIntergenicDistribution": 1.312109, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 6170, "distinctRankCount": 78, "maxRank": 18276.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 174727583, "mappedReadsCount": 127449240, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138877" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000980", "name": "plasmablast" }, "cellTypeAuthorAnnotation": "B_plasmablast, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 1315.793583, "sdRefIntergenicDistribution": 1.326979, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 715, "distinctRankCount": 11, "maxRank": 17748.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 174727583, "mappedReadsCount": 127449240, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138877" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0000232", "name": "erythrocyte" }, "cellTypeAuthorAnnotation": "Erythrocyte, Vascular", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 357.934366, "sdRefIntergenicDistribution": 1.254357, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 2840, "distinctRankCount": 25, "maxRank": 17909.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 174727583, "mappedReadsCount": 127449240, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138877" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0008953", "name": "lower lobe of left lung" }, "anatEntityAuthorAnnotation": "Lower Left Lobe", "cellType": { "id": "CL:0017000", "name": "pulmonary ionocyte" }, "cellTypeAuthorAnnotation": "Ionocyte_n_Brush, Epithelia", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 138.168322, "sdRefIntergenicDistribution": 1.242158, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 7437, "distinctRankCount": 67, "maxRank": 18708.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 172143794, "mappedReadsCount": 102290992, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138892" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000583", "name": "alveolar macrophage" }, "cellTypeAuthorAnnotation": "Macro_alveolar, Immune", "devStage": { "id": "HsapDv:0000123", "name": "29-year-old stage (human)" }, "devStageAuthorAnnotation": "25-30 (29 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 177.406391, "sdRefIntergenicDistribution": 1.476120, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 5974, "distinctRankCount": 73, "maxRank": 18457.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 172143794, "mappedReadsCount": 102290992, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138892" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0002553", "name": "fibroblast of lung" }, "cellTypeAuthorAnnotation": "Fibro_adventitial, Stroma", "devStage": { "id": "HsapDv:0000123", "name": "29-year-old stage (human)" }, "devStageAuthorAnnotation": "25-30 (29 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 21.368617, "sdRefIntergenicDistribution": 1.437426, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 51977, "distinctRankCount": 307, "maxRank": 20497.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 172143794, "mappedReadsCount": 102290992, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138892" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0002553", "name": "fibroblast of lung" }, "cellTypeAuthorAnnotation": "Fibro_alveolar, Stroma", "devStage": { "id": "HsapDv:0000123", "name": "29-year-old stage (human)" }, "devStageAuthorAnnotation": "25-30 (29 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 126.004024, "sdRefIntergenicDistribution": 1.290733, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 8080, "distinctRankCount": 67, "maxRank": 18652.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 172143794, "mappedReadsCount": 102290992, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138892" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0002553", "name": "fibroblast of lung" }, "cellTypeAuthorAnnotation": "Fibro_peribronchial, Stroma", "devStage": { "id": "HsapDv:0000123", "name": "29-year-old stage (human)" }, "devStageAuthorAnnotation": "25-30 (29 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 108.783146, "sdRefIntergenicDistribution": 1.321481, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 9621, "distinctRankCount": 114, "maxRank": 18816.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 172143794, "mappedReadsCount": 102290992, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138892" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0009115", "name": "lymph node lymphatic vessel endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_Lymphatic, Vascular", "devStage": { "id": "HsapDv:0000123", "name": "29-year-old stage (human)" }, "devStageAuthorAnnotation": "25-30 (29 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 11.759298, "sdRefIntergenicDistribution": 1.532028, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 99256, "distinctRankCount": 518, "maxRank": 21885.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 172143794, "mappedReadsCount": 102290992, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138892" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:1001568", "name": "pulmonary artery endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_arterial_pulmonary, Vascular", "devStage": { "id": "HsapDv:0000123", "name": "29-year-old stage (human)" }, "devStageAuthorAnnotation": "25-30 (29 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 325.683350, "sdRefIntergenicDistribution": 1.292507, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 2979, "distinctRankCount": 31, "maxRank": 18155.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 172143794, "mappedReadsCount": 102290992, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138892" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0002633", "name": "respiratory basal cell" }, "cellTypeAuthorAnnotation": "Basal, Epithelia", "devStage": { "id": "HsapDv:0000123", "name": "29-year-old stage (human)" }, "devStageAuthorAnnotation": "25-30 (29 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 50.701241, "sdRefIntergenicDistribution": 1.464016, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 21717, "distinctRankCount": 235, "maxRank": 19732.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 172143794, "mappedReadsCount": 102290992, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138892" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0002633", "name": "respiratory basal cell" }, "cellTypeAuthorAnnotation": "Dividing_Basal, Epithelia", "devStage": { "id": "HsapDv:0000123", "name": "29-year-old stage (human)" }, "devStageAuthorAnnotation": "25-30 (29 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 30.080655, "sdRefIntergenicDistribution": 1.579629, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 37154, "distinctRankCount": 295, "maxRank": 20641.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 172143794, "mappedReadsCount": 102290992, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138892" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:1001603", "name": "lung macrophage" }, "cellTypeAuthorAnnotation": "Macro_interstitial, Immune", "devStage": { "id": "HsapDv:0000123", "name": "29-year-old stage (human)" }, "devStageAuthorAnnotation": "25-30 (29 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 352.979092, "sdRefIntergenicDistribution": 1.228210, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 2928, "distinctRankCount": 38, "maxRank": 18051.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 172143794, "mappedReadsCount": 102290992, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138892" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0002144", "name": "capillary endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_Cap_a, Vascular", "devStage": { "id": "HsapDv:0000123", "name": "29-year-old stage (human)" }, "devStageAuthorAnnotation": "25-30 (29 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 100.509833, "sdRefIntergenicDistribution": 1.350630, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 10175, "distinctRankCount": 75, "maxRank": 18864.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 172143794, "mappedReadsCount": 102290992, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138892" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0002144", "name": "capillary endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_Cap_g, Vascular", "devStage": { "id": "HsapDv:0000123", "name": "29-year-old stage (human)" }, "devStageAuthorAnnotation": "25-30 (29 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 44.890780, "sdRefIntergenicDistribution": 1.430135, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 23848, "distinctRankCount": 234, "maxRank": 19887.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 172143794, "mappedReadsCount": 102290992, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138892" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000990", "name": "conventional dendritic cell" }, "cellTypeAuthorAnnotation": "DC_2, Immune", "devStage": { "id": "HsapDv:0000123", "name": "29-year-old stage (human)" }, "devStageAuthorAnnotation": "25-30 (29 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 216.722008, "sdRefIntergenicDistribution": 1.274964, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 4696, "distinctRankCount": 48, "maxRank": 18164.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 172143794, "mappedReadsCount": 102290992, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138892" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0002543", "name": "vein endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_venous_pulmonary, Vascular", "devStage": { "id": "HsapDv:0000123", "name": "29-year-old stage (human)" }, "devStageAuthorAnnotation": "25-30 (29 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 1247.451931, "sdRefIntergenicDistribution": 1.303424, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 752, "distinctRankCount": 14, "maxRank": 17758.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 172143794, "mappedReadsCount": 102290992, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138892" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0002543", "name": "vein endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_venous_systemic, Vascular", "devStage": { "id": "HsapDv:0000123", "name": "29-year-old stage (human)" }, "devStageAuthorAnnotation": "25-30 (29 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 293.757705, "sdRefIntergenicDistribution": 1.283181, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 3479, "distinctRankCount": 44, "maxRank": 18137.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 172143794, "mappedReadsCount": 102290992, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138892" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000160", "name": "goblet cell" }, "cellTypeAuthorAnnotation": "Secretory_Goblet, Epithelia", "devStage": { "id": "HsapDv:0000123", "name": "29-year-old stage (human)" }, "devStageAuthorAnnotation": "25-30 (29 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 38.833238, "sdRefIntergenicDistribution": 1.581759, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 30531, "distinctRankCount": 215, "maxRank": 19595.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 172143794, "mappedReadsCount": 102290992, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138892" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000798", "name": "gamma-delta T cell" }, "cellTypeAuthorAnnotation": "gdT, Immune", "devStage": { "id": "HsapDv:0000123", "name": "29-year-old stage (human)" }, "devStageAuthorAnnotation": "25-30 (29 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 605.884068, "sdRefIntergenicDistribution": 1.442478, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1542, "distinctRankCount": 20, "maxRank": 17846.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 172143794, "mappedReadsCount": 102290992, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138892" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000623", "name": "natural killer cell" }, "cellTypeAuthorAnnotation": "NK_CD16hi, Immune", "devStage": { "id": "HsapDv:0000123", "name": "29-year-old stage (human)" }, "devStageAuthorAnnotation": "25-30 (29 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 456.855440, "sdRefIntergenicDistribution": 1.203976, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 2078, "distinctRankCount": 32, "maxRank": 18000.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 172143794, "mappedReadsCount": 102290992, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138892" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000097", "name": "mast cell" }, "cellTypeAuthorAnnotation": "Mast_cell , Immune", "devStage": { "id": "HsapDv:0000123", "name": "29-year-old stage (human)" }, "devStageAuthorAnnotation": "25-30 (29 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 1056.175075, "sdRefIntergenicDistribution": 1.259685, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 954, "distinctRankCount": 18, "maxRank": 17779.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 172143794, "mappedReadsCount": 102290992, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138892" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000192", "name": "smooth muscle cell" }, "cellTypeAuthorAnnotation": "Muscle_smooth_pulmonary, Stroma", "devStage": { "id": "HsapDv:0000123", "name": "29-year-old stage (human)" }, "devStageAuthorAnnotation": "25-30 (29 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 156.068118, "sdRefIntergenicDistribution": 1.289856, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 6389, "distinctRankCount": 70, "maxRank": 18493.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 172143794, "mappedReadsCount": 102290992, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138892" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000067", "name": "ciliated epithelial cell" }, "cellTypeAuthorAnnotation": "Ciliated, Epithelia", "devStage": { "id": "HsapDv:0000123", "name": "29-year-old stage (human)" }, "devStageAuthorAnnotation": "25-30 (29 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 22.581220, "sdRefIntergenicDistribution": 1.654844, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 52564, "distinctRankCount": 494, "maxRank": 21262.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 172143794, "mappedReadsCount": 102290992, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138892" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0009089", "name": "lung pericyte" }, "cellTypeAuthorAnnotation": "Muscle_pericyte_pulmonary, Stroma", "devStage": { "id": "HsapDv:0000123", "name": "29-year-old stage (human)" }, "devStageAuthorAnnotation": "25-30 (29 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 321.481879, "sdRefIntergenicDistribution": 1.287951, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 3101, "distinctRankCount": 37, "maxRank": 18166.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 172143794, "mappedReadsCount": 102290992, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138892" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000186", "name": "myofibroblast cell" }, "cellTypeAuthorAnnotation": "Fibro_myofibroblast, Stroma", "devStage": { "id": "HsapDv:0000123", "name": "29-year-old stage (human)" }, "devStageAuthorAnnotation": "25-30 (29 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 113.197853, "sdRefIntergenicDistribution": 1.300319, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 8937, "distinctRankCount": 81, "maxRank": 18756.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 172143794, "mappedReadsCount": 102290992, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138892" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000985", "name": "IgG plasma cell" }, "cellTypeAuthorAnnotation": "B_plasma_IgG, Immune", "devStage": { "id": "HsapDv:0000123", "name": "29-year-old stage (human)" }, "devStageAuthorAnnotation": "25-30 (29 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 32.308528, "sdRefIntergenicDistribution": 1.609364, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 37246, "distinctRankCount": 94, "maxRank": 18544.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 172143794, "mappedReadsCount": 102290992, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138892" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000158", "name": "club cell" }, "cellTypeAuthorAnnotation": "Secretory_Club, Epithelia", "devStage": { "id": "HsapDv:0000123", "name": "29-year-old stage (human)" }, "devStageAuthorAnnotation": "25-30 (29 in HCA)", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 60.201047, "sdRefIntergenicDistribution": 1.507311, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 19445, "distinctRankCount": 97, "maxRank": 18618.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 421902905, "mappedReadsCount": 241027882, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138895" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:0000319", "name": "mucus secreting cell" }, "cellTypeAuthorAnnotation": "SMG_Mucous, Epithelia", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 0.912764, "sdRefIntergenicDistribution": 2.848908, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 4913566, "distinctRankCount": 7520, "maxRank": 27827.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 421902905, "mappedReadsCount": 241027882, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138895" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:0000138", "name": "chondrocyte" }, "cellTypeAuthorAnnotation": "Chondrocyte, Stroma", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 2.487627, "sdRefIntergenicDistribution": 2.030695, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 668352, "distinctRankCount": 4205, "maxRank": 25668.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 421902905, "mappedReadsCount": 241027882, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138895" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:1001603", "name": "lung macrophage" }, "cellTypeAuthorAnnotation": "Macro_CHIT1, Immune", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 30.320404, "sdRefIntergenicDistribution": 1.403445, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 35357, "distinctRankCount": 1640, "maxRank": 20940.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 421902905, "mappedReadsCount": 241027882, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138895" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:1001603", "name": "lung macrophage" }, "cellTypeAuthorAnnotation": "Macro_dividing, Immune", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 1524.546254, "sdRefIntergenicDistribution": 1.262970, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 673, "distinctRankCount": 63, "maxRank": 17811.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 421902905, "mappedReadsCount": 241027882, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138895" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:1001603", "name": "lung macrophage" }, "cellTypeAuthorAnnotation": "Macro_intermediate, Immune", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 307.265270, "sdRefIntergenicDistribution": 1.155662, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 3161, "distinctRankCount": 198, "maxRank": 18301.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 421902905, "mappedReadsCount": 241027882, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138895" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:1001603", "name": "lung macrophage" }, "cellTypeAuthorAnnotation": "Macro_interstitial, Immune", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 151.026143, "sdRefIntergenicDistribution": 1.259887, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 6695, "distinctRankCount": 428, "maxRank": 18614.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 421902905, "mappedReadsCount": 241027882, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138895" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:1001603", "name": "lung macrophage" }, "cellTypeAuthorAnnotation": "Macro_intravascular, Immune", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 9.261742, "sdRefIntergenicDistribution": 1.638132, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 130265, "distinctRankCount": 2734, "maxRank": 23138.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 421902905, "mappedReadsCount": 241027882, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138895" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:0000160", "name": "goblet cell" }, "cellTypeAuthorAnnotation": "Secretory_Goblet, Epithelia", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 5.889326, "sdRefIntergenicDistribution": 1.661702, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 212554, "distinctRankCount": 3445, "maxRank": 23757.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 421902905, "mappedReadsCount": 241027882, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138895" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:0000623", "name": "natural killer cell" }, "cellTypeAuthorAnnotation": "NK_CD11d, Immune", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 2013.716432, "sdRefIntergenicDistribution": 1.162938, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 475, "distinctRankCount": 18, "maxRank": 17737.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 421902905, "mappedReadsCount": 241027882, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138895" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:0000623", "name": "natural killer cell" }, "cellTypeAuthorAnnotation": "NK_CD16hi, Immune", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 308.170982, "sdRefIntergenicDistribution": 1.231504, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 3191, "distinctRankCount": 180, "maxRank": 18399.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 421902905, "mappedReadsCount": 241027882, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138895" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:0000623", "name": "natural killer cell" }, "cellTypeAuthorAnnotation": "NK_CD56bright, Immune", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 1396.433239, "sdRefIntergenicDistribution": 1.236872, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 728, "distinctRankCount": 32, "maxRank": 17790.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 421902905, "mappedReadsCount": 241027882, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138895" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:0000158", "name": "club cell" }, "cellTypeAuthorAnnotation": "Secretory_Club, Epithelia", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 30.802892, "sdRefIntergenicDistribution": 1.394441, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 35046, "distinctRankCount": 1677, "maxRank": 21047.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 421902905, "mappedReadsCount": 241027882, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138895" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:0000909", "name": "CD8-positive, alpha-beta memory T cell" }, "cellTypeAuthorAnnotation": "CD8_TRM, Immune", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 8.588016, "sdRefIntergenicDistribution": 1.616841, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 139639, "distinctRankCount": 2405, "maxRank": 23068.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 421902905, "mappedReadsCount": 241027882, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138895" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:0000909", "name": "CD8-positive, alpha-beta memory T cell" }, "cellTypeAuthorAnnotation": "CD8_TRM/EM, Immune", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 27.095093, "sdRefIntergenicDistribution": 1.495184, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 40476, "distinctRankCount": 1367, "maxRank": 20819.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 421902905, "mappedReadsCount": 241027882, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138895" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:0002553", "name": "fibroblast of lung" }, "cellTypeAuthorAnnotation": "Fibro_adventitial, Stroma", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 1.679829, "sdRefIntergenicDistribution": 2.115312, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1125664, "distinctRankCount": 4940, "maxRank": 26499.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 421902905, "mappedReadsCount": 241027882, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138895" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:0002553", "name": "fibroblast of lung" }, "cellTypeAuthorAnnotation": "Fibro_alveolar, Stroma", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 1.975240, "sdRefIntergenicDistribution": 2.050736, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 898810, "distinctRankCount": 4925, "maxRank": 26182.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 421902905, "mappedReadsCount": 241027882, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138895" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:0002553", "name": "fibroblast of lung" }, "cellTypeAuthorAnnotation": "Fibro_peribronchial, Stroma", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 3.834226, "sdRefIntergenicDistribution": 1.789884, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 362680, "distinctRankCount": 3897, "maxRank": 25077.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 421902905, "mappedReadsCount": 241027882, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138895" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:0002553", "name": "fibroblast of lung" }, "cellTypeAuthorAnnotation": "Fibro_perichondrial, Stroma", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 4.951416, "sdRefIntergenicDistribution": 1.695370, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 260007, "distinctRankCount": 3211, "maxRank": 24207.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 421902905, "mappedReadsCount": 241027882, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138895" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:0000787", "name": "memory B cell" }, "cellTypeAuthorAnnotation": "B_memory, Immune", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 36.005573, "sdRefIntergenicDistribution": 1.434102, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 29608, "distinctRankCount": 1159, "maxRank": 20357.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 421902905, "mappedReadsCount": 241027882, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138895" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:0000985", "name": "IgG plasma cell" }, "cellTypeAuthorAnnotation": "B_plasma_IgG, Immune", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 21.872385, "sdRefIntergenicDistribution": 1.547521, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 51044, "distinctRankCount": 1744, "maxRank": 21221.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 421902905, "mappedReadsCount": 241027882, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138895" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:0002633", "name": "respiratory basal cell" }, "cellTypeAuthorAnnotation": "Basal, Epithelia", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 2.377172, "sdRefIntergenicDistribution": 2.030555, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 710545, "distinctRankCount": 4784, "maxRank": 26165.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 421902905, "mappedReadsCount": 241027882, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138895" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:0002633", "name": "respiratory basal cell" }, "cellTypeAuthorAnnotation": "Dividing_Basal, Epithelia", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 30.536865, "sdRefIntergenicDistribution": 1.336809, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 34325, "distinctRankCount": 1749, "maxRank": 21207.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 421902905, "mappedReadsCount": 241027882, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138895" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:0002633", "name": "respiratory basal cell" }, "cellTypeAuthorAnnotation": "SMG_Basal, Epithelia", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 96.227095, "sdRefIntergenicDistribution": 1.413938, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 11011, "distinctRankCount": 814, "maxRank": 19184.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 421902905, "mappedReadsCount": 241027882, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138895" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:0000990", "name": "conventional dendritic cell" }, "cellTypeAuthorAnnotation": "DC_1, Immune", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 122.246711, "sdRefIntergenicDistribution": 1.431310, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 8714, "distinctRankCount": 520, "maxRank": 18861.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 421902905, "mappedReadsCount": 241027882, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138895" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:0000990", "name": "conventional dendritic cell" }, "cellTypeAuthorAnnotation": "DC_2, Immune", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 45.350021, "sdRefIntergenicDistribution": 1.373520, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 23334, "distinctRankCount": 1335, "maxRank": 20164.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 421902905, "mappedReadsCount": 241027882, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138895" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:0000990", "name": "conventional dendritic cell" }, "cellTypeAuthorAnnotation": "DC_activated, Immune", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 176.260164, "sdRefIntergenicDistribution": 1.298078, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 5882, "distinctRankCount": 369, "maxRank": 18585.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 421902905, "mappedReadsCount": 241027882, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138895" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:0000097", "name": "mast cell" }, "cellTypeAuthorAnnotation": "Mast_cell , Immune", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 11.060430, "sdRefIntergenicDistribution": 1.675820, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 108107, "distinctRankCount": 2399, "maxRank": 22626.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 421902905, "mappedReadsCount": 241027882, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138895" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:0000815", "name": "regulatory T cell" }, "cellTypeAuthorAnnotation": "T_reg, Immune", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 22.615348, "sdRefIntergenicDistribution": 1.445068, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 48133, "distinctRankCount": 1602, "maxRank": 21340.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 421902905, "mappedReadsCount": 241027882, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138895" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:0000192", "name": "smooth muscle cell" }, "cellTypeAuthorAnnotation": "Muscle_smooth_pulmonary, Stroma", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 34.491920, "sdRefIntergenicDistribution": 1.301256, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 29943, "distinctRankCount": 1321, "maxRank": 20366.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 421902905, "mappedReadsCount": 241027882, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138895" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:0000897", "name": "CD4-positive, alpha-beta memory T cell" }, "cellTypeAuthorAnnotation": "CD4_TRM, Immune", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 526.451124, "sdRefIntergenicDistribution": 1.175069, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1860, "distinctRankCount": 98, "maxRank": 18089.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 421902905, "mappedReadsCount": 241027882, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138895" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:0000235", "name": "macrophage" }, "cellTypeAuthorAnnotation": "Macro_AW_CX3CR1, Immune", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 9.417496, "sdRefIntergenicDistribution": 1.566634, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 125639, "distinctRankCount": 2714, "maxRank": 23077.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 421902905, "mappedReadsCount": 241027882, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138895" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:0000067", "name": "ciliated epithelial cell" }, "cellTypeAuthorAnnotation": "Ciliated, Epithelia", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 17.774850, "sdRefIntergenicDistribution": 1.849854, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 70700, "distinctRankCount": 2373, "maxRank": 21891.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 421902905, "mappedReadsCount": 241027882, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138895" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:0001054", "name": "CD14-positive monocyte" }, "cellTypeAuthorAnnotation": "Monocyte_CD14, Immune", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 44.197039, "sdRefIntergenicDistribution": 1.395290, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 24272, "distinctRankCount": 1250, "maxRank": 20232.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 421902905, "mappedReadsCount": 241027882, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138895" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:0000987", "name": "IgA plasma cell" }, "cellTypeAuthorAnnotation": "B_plasma_IgA, Immune", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 6.703076, "sdRefIntergenicDistribution": 1.735692, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 188657, "distinctRankCount": 2935, "maxRank": 23546.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 421902905, "mappedReadsCount": 241027882, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138895" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:0000146", "name": "simple columnar epithelial cell" }, "cellTypeAuthorAnnotation": "SMG_Duct, Epithelia", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 9.492455, "sdRefIntergenicDistribution": 1.494040, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 120867, "distinctRankCount": 2663, "maxRank": 22787.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 421902905, "mappedReadsCount": 241027882, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138895" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:0000624", "name": "CD4-positive, alpha-beta T cell" }, "cellTypeAuthorAnnotation": "CD4_EM/Effector, Immune", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 13.694056, "sdRefIntergenicDistribution": 1.543409, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 83007, "distinctRankCount": 1974, "maxRank": 22233.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 421902905, "mappedReadsCount": 241027882, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138895" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:0000624", "name": "CD4-positive, alpha-beta T cell" }, "cellTypeAuthorAnnotation": "CD4_naive/CM, Immune", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 9.664498, "sdRefIntergenicDistribution": 1.595496, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 121787, "distinctRankCount": 2372, "maxRank": 23076.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 421902905, "mappedReadsCount": 241027882, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138895" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:0000583", "name": "alveolar macrophage" }, "cellTypeAuthorAnnotation": "Macro_alveolar, Immune", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 231.663127, "sdRefIntergenicDistribution": 1.397495, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 4519, "distinctRankCount": 301, "maxRank": 18607.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 421902905, "mappedReadsCount": 241027882, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138895" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:0017000", "name": "pulmonary ionocyte" }, "cellTypeAuthorAnnotation": "Ionocyte_n_Brush, Epithelia", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 54.166552, "sdRefIntergenicDistribution": 1.390094, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 19531, "distinctRankCount": 1284, "maxRank": 20060.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 421902905, "mappedReadsCount": 241027882, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138895" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:0000798", "name": "gamma-delta T cell" }, "cellTypeAuthorAnnotation": "gdT, Immune", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 225.004997, "sdRefIntergenicDistribution": 1.403497, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 4751, "distinctRankCount": 279, "maxRank": 18545.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 421902905, "mappedReadsCount": 241027882, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138895" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:0002144", "name": "capillary endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_Cap_g, Vascular", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 580.016722, "sdRefIntergenicDistribution": 1.489638, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1781, "distinctRankCount": 109, "maxRank": 18006.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 421902905, "mappedReadsCount": 241027882, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138895" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:0002368", "name": "respiratory epithelial cell" }, "cellTypeAuthorAnnotation": "Suprabasal, Epithelia", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 3.333110, "sdRefIntergenicDistribution": 1.816343, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 432682, "distinctRankCount": 4255, "maxRank": 25214.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 421902905, "mappedReadsCount": 241027882, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138895" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:0000940", "name": "mucosal invariant T cell" }, "cellTypeAuthorAnnotation": "MAIT, Immune", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 207.127985, "sdRefIntergenicDistribution": 1.276128, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 4859, "distinctRankCount": 365, "maxRank": 18529.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 421902905, "mappedReadsCount": 241027882, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138895" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:0000057", "name": "fibroblast" }, "cellTypeAuthorAnnotation": "NAF_endoneurial, Stroma", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 68.260827, "sdRefIntergenicDistribution": 1.332246, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 15300, "distinctRankCount": 890, "maxRank": 19455.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 421902905, "mappedReadsCount": 241027882, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138895" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:0000057", "name": "fibroblast" }, "cellTypeAuthorAnnotation": "NAF_perineurial, Stroma", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 10.704977, "sdRefIntergenicDistribution": 1.488556, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 105010, "distinctRankCount": 2463, "maxRank": 22431.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 421902905, "mappedReadsCount": 241027882, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138895" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:0019018", "name": "blood vessel smooth muscle cell" }, "cellTypeAuthorAnnotation": "Muscle_perivascular_immune_recruiting, Stroma", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 23.813915, "sdRefIntergenicDistribution": 1.416969, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 45219, "distinctRankCount": 1617, "maxRank": 20787.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 421902905, "mappedReadsCount": 241027882, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138895" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:0019018", "name": "blood vessel smooth muscle cell" }, "cellTypeAuthorAnnotation": "Muscle_smooth_arterial_systemic, Stroma", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 23.477329, "sdRefIntergenicDistribution": 1.343096, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 44990, "distinctRankCount": 1663, "maxRank": 20852.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 421902905, "mappedReadsCount": 241027882, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138895" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:0002543", "name": "vein endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_venous_pulmonary, Vascular", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 122.264449, "sdRefIntergenicDistribution": 1.254713, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 8239, "distinctRankCount": 593, "maxRank": 18734.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 421902905, "mappedReadsCount": 241027882, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138895" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:0002543", "name": "vein endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_venous_systemic, Vascular", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 25.107270, "sdRefIntergenicDistribution": 1.390792, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 42757, "distinctRankCount": 1747, "maxRank": 21024.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 421902905, "mappedReadsCount": 241027882, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138895" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:0000788", "name": "naive B cell" }, "cellTypeAuthorAnnotation": "B_naive, Immune", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 226.443306, "sdRefIntergenicDistribution": 1.208945, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 4380, "distinctRankCount": 311, "maxRank": 18460.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 421902905, "mappedReadsCount": 241027882, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138895" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:1000413", "name": "endothelial cell of artery" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_arterial_systemic, Vascular", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 48.101337, "sdRefIntergenicDistribution": 1.344195, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 22095, "distinctRankCount": 1123, "maxRank": 19900.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 421902905, "mappedReadsCount": 241027882, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138895" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:0019001", "name": "tracheobronchial serous cell" }, "cellTypeAuthorAnnotation": "SMG_Serous, Epithelia", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 0.951049, "sdRefIntergenicDistribution": 2.625597, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 3532359, "distinctRankCount": 6806, "maxRank": 27490.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 421902905, "mappedReadsCount": 241027882, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138895" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:0009115", "name": "lymph node lymphatic vessel endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_Lymphatic, Vascular", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 66.592289, "sdRefIntergenicDistribution": 1.319568, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 15560, "distinctRankCount": 889, "maxRank": 19581.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 421902905, "mappedReadsCount": 241027882, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138895" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:0000980", "name": "plasmablast" }, "cellTypeAuthorAnnotation": "B_plasmablast, Immune", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 156.002351, "sdRefIntergenicDistribution": 1.432961, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 6897, "distinctRankCount": 493, "maxRank": 18736.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 421902905, "mappedReadsCount": 241027882, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138895" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:0019019", "name": "tracheobronchial smooth muscle cell" }, "cellTypeAuthorAnnotation": "Muscle_smooth_airway, Stroma", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 8.752880, "sdRefIntergenicDistribution": 1.485995, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 131683, "distinctRankCount": 2583, "maxRank": 22334.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 421902905, "mappedReadsCount": 241027882, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138895" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:0000669", "name": "pericyte cell" }, "cellTypeAuthorAnnotation": "Muscle_pericyte_systemic, Stroma", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 58.484543, "sdRefIntergenicDistribution": 1.381034, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 18177, "distinctRankCount": 933, "maxRank": 19667.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 421902905, "mappedReadsCount": 241027882, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138895" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:0000186", "name": "myofibroblast cell" }, "cellTypeAuthorAnnotation": "Fibro_myofibroblast, Stroma", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 364.514430, "sdRefIntergenicDistribution": 1.202301, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 2709, "distinctRankCount": 129, "maxRank": 18208.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 421902905, "mappedReadsCount": 241027882, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138895" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:0000077", "name": "mesothelial cell" }, "cellTypeAuthorAnnotation": "Mesothelia, Stroma", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 1031.528312, "sdRefIntergenicDistribution": 1.270896, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1004, "distinctRankCount": 36, "maxRank": 17845.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 421902905, "mappedReadsCount": 241027882, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138895" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:0002396", "name": "CD14-low, CD16-positive monocyte" }, "cellTypeAuthorAnnotation": "Monocyte_CD16, Immune", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 58.901449, "sdRefIntergenicDistribution": 1.348297, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 17628, "distinctRankCount": 991, "maxRank": 19955.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 421902905, "mappedReadsCount": 241027882, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138895" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:0000185", "name": "myoepithelial cell" }, "cellTypeAuthorAnnotation": "Myoepithelial, Epithelia", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 10.616959, "sdRefIntergenicDistribution": 1.535365, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 110178, "distinctRankCount": 2582, "maxRank": 22700.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 421902905, "mappedReadsCount": 241027882, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138895" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:0001065", "name": "innate lymphoid cell" }, "cellTypeAuthorAnnotation": "ILC, Immune", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 323.394655, "sdRefIntergenicDistribution": 1.358780, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 3188, "distinctRankCount": 118, "maxRank": 18331.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 421902905, "mappedReadsCount": 241027882, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138895" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:0000913", "name": "effector memory CD8-positive, alpha-beta T cell" }, "cellTypeAuthorAnnotation": "CD8_EM, Immune", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 30.646437, "sdRefIntergenicDistribution": 1.441319, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 34267, "distinctRankCount": 1235, "maxRank": 20583.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 421902905, "mappedReadsCount": 241027882, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138895" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:0000913", "name": "effector memory CD8-positive, alpha-beta T cell" }, "cellTypeAuthorAnnotation": "CD8_EM/EMRA, Immune", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 26.583243, "sdRefIntergenicDistribution": 1.497201, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 40976, "distinctRankCount": 1433, "maxRank": 20962.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 421902905, "mappedReadsCount": 241027882, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138895" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:1001568", "name": "pulmonary artery endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_arterial_pulmonary, Vascular", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 48.401943, "sdRefIntergenicDistribution": 1.372849, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 21698, "distinctRankCount": 996, "maxRank": 19989.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 421902905, "mappedReadsCount": 241027882, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138895" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:0002376", "name": "non-myelinating Schwann cell" }, "cellTypeAuthorAnnotation": "Schwann_nonmyelinating, Stroma", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 91.278965, "sdRefIntergenicDistribution": 1.224170, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 10932, "distinctRankCount": 640, "maxRank": 19215.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 421902905, "mappedReadsCount": 241027882, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138895" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:0009089", "name": "lung pericyte" }, "cellTypeAuthorAnnotation": "Muscle_pericyte_pulmonary, Stroma", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 269.986574, "sdRefIntergenicDistribution": 1.361849, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 3935, "distinctRankCount": 283, "maxRank": 18339.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "NUCLEUS", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 421902905, "mappedReadsCount": 241027882, "minReadLength": 91, "maxReadLength": 91 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138895" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002185", "name": "bronchus" }, "anatEntityAuthorAnnotation": "Bronchi 2-3 divison without surrounding parenchyma", "cellType": { "id": "CL:0000784", "name": "plasmacytoid dendritic cell" }, "cellTypeAuthorAnnotation": "DC_plasmacytoid, Immune", "devStage": { "id": "HsapDv:0000241", "name": "seventh decade stage (human)" }, "devStageAuthorAnnotation": "60-64", "sex": "male", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 158.944644, "sdRefIntergenicDistribution": 1.284227, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 6454, "distinctRankCount": 483, "maxRank": 18813.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 176082157, "mappedReadsCount": 121380701, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138899" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0002144", "name": "capillary endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_Cap_a, Vascular", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 13.189770, "sdRefIntergenicDistribution": 1.506676, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 87247, "distinctRankCount": 307, "maxRank": 21798.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 176082157, "mappedReadsCount": 121380701, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138899" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0002144", "name": "capillary endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_Cap_g, Vascular", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 4.035159, "sdRefIntergenicDistribution": 1.807281, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 361169, "distinctRankCount": 698, "maxRank": 23598.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 176082157, "mappedReadsCount": 121380701, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138899" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0001054", "name": "CD14-positive monocyte" }, "cellTypeAuthorAnnotation": "Monocyte_CD14, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 44.888322, "sdRefIntergenicDistribution": 1.417464, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 24110, "distinctRankCount": 160, "maxRank": 19398.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 176082157, "mappedReadsCount": 121380701, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138899" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0002396", "name": "CD14-low, CD16-positive monocyte" }, "cellTypeAuthorAnnotation": "Monocyte_CD16, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 47.651852, "sdRefIntergenicDistribution": 1.369702, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 22356, "distinctRankCount": 177, "maxRank": 19506.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 176082157, "mappedReadsCount": 121380701, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138899" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0002543", "name": "vein endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_venous_pulmonary, Vascular", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 8.458186, "sdRefIntergenicDistribution": 1.547772, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 140077, "distinctRankCount": 476, "maxRank": 22253.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 176082157, "mappedReadsCount": 121380701, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138899" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0002543", "name": "vein endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_venous_systemic, Vascular", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 2.682570, "sdRefIntergenicDistribution": 1.910122, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 602991, "distinctRankCount": 1154, "maxRank": 24030.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 176082157, "mappedReadsCount": 121380701, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138899" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0002553", "name": "fibroblast of lung" }, "cellTypeAuthorAnnotation": "Fibro_adventitial, Stroma", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 2.119869, "sdRefIntergenicDistribution": 2.302009, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1098730, "distinctRankCount": 1383, "maxRank": 25057.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 176082157, "mappedReadsCount": 121380701, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138899" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0002553", "name": "fibroblast of lung" }, "cellTypeAuthorAnnotation": "Fibro_alveolar, Stroma", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 9.817154, "sdRefIntergenicDistribution": 1.551316, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 121712, "distinctRankCount": 454, "maxRank": 22369.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 176082157, "mappedReadsCount": 121380701, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138899" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0002553", "name": "fibroblast of lung" }, "cellTypeAuthorAnnotation": "Fibro_immune_recruiting, Stroma", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 69.478735, "sdRefIntergenicDistribution": 1.266546, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 14470, "distinctRankCount": 116, "maxRank": 19187.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 176082157, "mappedReadsCount": 121380701, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138899" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0002553", "name": "fibroblast of lung" }, "cellTypeAuthorAnnotation": "Fibro_peribronchial, Stroma", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 11.149278, "sdRefIntergenicDistribution": 1.528497, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 104924, "distinctRankCount": 410, "maxRank": 22263.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 176082157, "mappedReadsCount": 121380701, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138899" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000623", "name": "natural killer cell" }, "cellTypeAuthorAnnotation": "NK_CD16hi, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 29.429356, "sdRefIntergenicDistribution": 1.395511, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 36423, "distinctRankCount": 203, "maxRank": 20501.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 176082157, "mappedReadsCount": 121380701, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138899" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000623", "name": "natural killer cell" }, "cellTypeAuthorAnnotation": "NK_CD56bright, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 123.393551, "sdRefIntergenicDistribution": 1.392753, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 8377, "distinctRankCount": 93, "maxRank": 18697.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 176082157, "mappedReadsCount": 121380701, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138899" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:1001603", "name": "lung macrophage" }, "cellTypeAuthorAnnotation": "Macro_CHIT1, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 26.105115, "sdRefIntergenicDistribution": 1.553000, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 44545, "distinctRankCount": 265, "maxRank": 20105.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 176082157, "mappedReadsCount": 121380701, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138899" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:1001603", "name": "lung macrophage" }, "cellTypeAuthorAnnotation": "Macro_interstitial, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 128.964050, "sdRefIntergenicDistribution": 1.324417, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 8259, "distinctRankCount": 85, "maxRank": 18673.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 176082157, "mappedReadsCount": 121380701, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138899" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:1001603", "name": "lung macrophage" }, "cellTypeAuthorAnnotation": "Macro_intravascular, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 23.323174, "sdRefIntergenicDistribution": 1.414382, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 47267, "distinctRankCount": 261, "maxRank": 20595.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 176082157, "mappedReadsCount": 121380701, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138899" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000158", "name": "club cell" }, "cellTypeAuthorAnnotation": "Secretory_Club, Epithelia", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 23.686664, "sdRefIntergenicDistribution": 1.636785, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 49686, "distinctRankCount": 322, "maxRank": 20657.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 176082157, "mappedReadsCount": 121380701, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138899" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000097", "name": "mast cell" }, "cellTypeAuthorAnnotation": "Mast_cell , Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 213.257154, "sdRefIntergenicDistribution": 1.281688, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 4833, "distinctRankCount": 52, "maxRank": 18300.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 176082157, "mappedReadsCount": 121380701, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138899" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000814", "name": "mature NK T cell" }, "cellTypeAuthorAnnotation": "NKT, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 20.212315, "sdRefIntergenicDistribution": 1.468512, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 54902, "distinctRankCount": 254, "maxRank": 20813.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 176082157, "mappedReadsCount": 121380701, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138899" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0002633", "name": "respiratory basal cell" }, "cellTypeAuthorAnnotation": "Basal, Epithelia", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 1.270917, "sdRefIntergenicDistribution": 2.750048, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 3180112, "distinctRankCount": 3201, "maxRank": 26429.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 176082157, "mappedReadsCount": 121380701, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138899" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0002633", "name": "respiratory basal cell" }, "cellTypeAuthorAnnotation": "Dividing_Basal, Epithelia", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 4.831713, "sdRefIntergenicDistribution": 1.787835, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 292560, "distinctRankCount": 1045, "maxRank": 23533.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 176082157, "mappedReadsCount": 121380701, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138899" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0002633", "name": "respiratory basal cell" }, "cellTypeAuthorAnnotation": "SMG_Basal, Epithelia", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 5.042738, "sdRefIntergenicDistribution": 1.799946, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 281689, "distinctRankCount": 920, "maxRank": 23590.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 176082157, "mappedReadsCount": 121380701, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138899" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000624", "name": "CD4-positive, alpha-beta T cell" }, "cellTypeAuthorAnnotation": "CD4_EM/Effector, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 12.044788, "sdRefIntergenicDistribution": 1.697858, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 101946, "distinctRankCount": 351, "maxRank": 21672.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 176082157, "mappedReadsCount": 121380701, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138899" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000624", "name": "CD4-positive, alpha-beta T cell" }, "cellTypeAuthorAnnotation": "CD4_naive/CM, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 19.789956, "sdRefIntergenicDistribution": 1.576576, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 56942, "distinctRankCount": 264, "maxRank": 20916.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 176082157, "mappedReadsCount": 121380701, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138899" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000897", "name": "CD4-positive, alpha-beta memory T cell" }, "cellTypeAuthorAnnotation": "CD4_TRM, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 29.628965, "sdRefIntergenicDistribution": 1.528307, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 37294, "distinctRankCount": 201, "maxRank": 20328.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 176082157, "mappedReadsCount": 121380701, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138899" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0019018", "name": "blood vessel smooth muscle cell" }, "cellTypeAuthorAnnotation": "Muscle_perivascular_immune_recruiting, Stroma", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 65.961042, "sdRefIntergenicDistribution": 1.367211, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 16419, "distinctRankCount": 136, "maxRank": 19091.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 176082157, "mappedReadsCount": 121380701, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138899" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0019018", "name": "blood vessel smooth muscle cell" }, "cellTypeAuthorAnnotation": "Muscle_smooth_arterial_systemic, Stroma", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 39.938296, "sdRefIntergenicDistribution": 1.403844, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 26953, "distinctRankCount": 165, "maxRank": 19744.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 176082157, "mappedReadsCount": 121380701, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138899" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000186", "name": "myofibroblast cell" }, "cellTypeAuthorAnnotation": "Fibro_myofibroblast, Stroma", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 22.681454, "sdRefIntergenicDistribution": 1.442194, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 47958, "distinctRankCount": 249, "maxRank": 21123.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 176082157, "mappedReadsCount": 121380701, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138899" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000909", "name": "CD8-positive, alpha-beta memory T cell" }, "cellTypeAuthorAnnotation": "CD8_TRM, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 103.529078, "sdRefIntergenicDistribution": 1.355491, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 9503, "distinctRankCount": 87, "maxRank": 18803.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 176082157, "mappedReadsCount": 121380701, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138899" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000909", "name": "CD8-positive, alpha-beta memory T cell" }, "cellTypeAuthorAnnotation": "CD8_TRM/EM, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 21.058981, "sdRefIntergenicDistribution": 1.588308, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 53870, "distinctRankCount": 237, "maxRank": 20800.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 176082157, "mappedReadsCount": 121380701, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138899" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000583", "name": "alveolar macrophage" }, "cellTypeAuthorAnnotation": "Macro_alveolar, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 15.549153, "sdRefIntergenicDistribution": 1.486216, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 75040, "distinctRankCount": 317, "maxRank": 20620.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 176082157, "mappedReadsCount": 121380701, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138899" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000815", "name": "regulatory T cell" }, "cellTypeAuthorAnnotation": "T_reg, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 115.481920, "sdRefIntergenicDistribution": 1.292196, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 8557, "distinctRankCount": 81, "maxRank": 18761.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 176082157, "mappedReadsCount": 121380701, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138899" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000160", "name": "goblet cell" }, "cellTypeAuthorAnnotation": "Secretory_Goblet, Epithelia", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 2.559531, "sdRefIntergenicDistribution": 1.965668, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 646267, "distinctRankCount": 1252, "maxRank": 23940.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 176082157, "mappedReadsCount": 121380701, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138899" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0001065", "name": "innate lymphoid cell" }, "cellTypeAuthorAnnotation": "ILC, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 450.443973, "sdRefIntergenicDistribution": 1.571986, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 2237, "distinctRankCount": 31, "maxRank": 17989.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 176082157, "mappedReadsCount": 121380701, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138899" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000192", "name": "smooth muscle cell" }, "cellTypeAuthorAnnotation": "Muscle_smooth_pulmonary, Stroma", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 4.759299, "sdRefIntergenicDistribution": 1.563521, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 260326, "distinctRankCount": 650, "maxRank": 23184.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 176082157, "mappedReadsCount": 121380701, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138899" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:1001568", "name": "pulmonary artery endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_arterial_pulmonary, Vascular", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 6.019654, "sdRefIntergenicDistribution": 1.703201, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 217176, "distinctRankCount": 623, "maxRank": 22970.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 176082157, "mappedReadsCount": 121380701, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138899" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000787", "name": "memory B cell" }, "cellTypeAuthorAnnotation": "B_memory, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 143.107702, "sdRefIntergenicDistribution": 1.205164, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 6854, "distinctRankCount": 87, "maxRank": 18477.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 176082157, "mappedReadsCount": 121380701, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138899" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000913", "name": "effector memory CD8-positive, alpha-beta T cell" }, "cellTypeAuthorAnnotation": "CD8_EM, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 22.095547, "sdRefIntergenicDistribution": 1.586244, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 50676, "distinctRankCount": 241, "maxRank": 20630.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 176082157, "mappedReadsCount": 121380701, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138899" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000913", "name": "effector memory CD8-positive, alpha-beta T cell" }, "cellTypeAuthorAnnotation": "CD8_EM/EMRA, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 32.483093, "sdRefIntergenicDistribution": 1.389018, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 32729, "distinctRankCount": 191, "maxRank": 20123.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 176082157, "mappedReadsCount": 121380701, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138899" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000985", "name": "IgG plasma cell" }, "cellTypeAuthorAnnotation": "B_plasma_IgG, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 17.875871, "sdRefIntergenicDistribution": 1.575277, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 64905, "distinctRankCount": 168, "maxRank": 19543.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 176082157, "mappedReadsCount": 121380701, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138899" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000987", "name": "IgA plasma cell" }, "cellTypeAuthorAnnotation": "B_plasma_IgA, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 8.236118, "sdRefIntergenicDistribution": 1.680764, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 148763, "distinctRankCount": 295, "maxRank": 20717.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 176082157, "mappedReadsCount": 121380701, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138899" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0009115", "name": "lymph node lymphatic vessel endothelial cell" }, "cellTypeAuthorAnnotation": "Endothelia_Lymphatic, Vascular", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 7.998046, "sdRefIntergenicDistribution": 1.529988, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 150657, "distinctRankCount": 554, "maxRank": 22511.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 176082157, "mappedReadsCount": 121380701, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138899" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0002368", "name": "respiratory epithelial cell" }, "cellTypeAuthorAnnotation": "Suprabasal, Epithelia", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 1.663723, "sdRefIntergenicDistribution": 2.326561, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1398089, "distinctRankCount": 2081, "maxRank": 25298.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 176082157, "mappedReadsCount": 121380701, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138899" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000067", "name": "ciliated epithelial cell" }, "cellTypeAuthorAnnotation": "Ciliated, Epithelia", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 5.678799, "sdRefIntergenicDistribution": 1.949218, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 274141, "distinctRankCount": 1238, "maxRank": 23853.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 176082157, "mappedReadsCount": 121380701, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138899" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000940", "name": "mucosal invariant T cell" }, "cellTypeAuthorAnnotation": "MAIT, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 54.411477, "sdRefIntergenicDistribution": 1.582545, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 19840, "distinctRankCount": 165, "maxRank": 19308.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 176082157, "mappedReadsCount": 121380701, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138899" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0009089", "name": "lung pericyte" }, "cellTypeAuthorAnnotation": "Muscle_pericyte_pulmonary, Stroma", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 8.236547, "sdRefIntergenicDistribution": 1.615057, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 151534, "distinctRankCount": 447, "maxRank": 22669.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 176082157, "mappedReadsCount": 121380701, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138899" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:1000413", "name": "endothelial cell of artery" }, "cellTypeAuthorAnnotation": "Endothelia_vascular_arterial_systemic, Vascular", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 42.887817, "sdRefIntergenicDistribution": 1.383043, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 24370, "distinctRankCount": 170, "maxRank": 20107.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 176082157, "mappedReadsCount": 121380701, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138899" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000235", "name": "macrophage" }, "cellTypeAuthorAnnotation": "Macro_AW_CX3CR1, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 55.719635, "sdRefIntergenicDistribution": 1.501794, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 20468, "distinctRankCount": 151, "maxRank": 19465.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 176082157, "mappedReadsCount": 121380701, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138899" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000669", "name": "pericyte cell" }, "cellTypeAuthorAnnotation": "Muscle_pericyte_systemic, Stroma", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 145.297077, "sdRefIntergenicDistribution": 1.304043, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 7118, "distinctRankCount": 63, "maxRank": 18616.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 176082157, "mappedReadsCount": 121380701, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138899" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000077", "name": "mesothelial cell" }, "cellTypeAuthorAnnotation": "Mesothelia, Stroma", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 649.690506, "sdRefIntergenicDistribution": 1.373043, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1463, "distinctRankCount": 24, "maxRank": 17925.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 176082157, "mappedReadsCount": 121380701, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138899" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000057", "name": "fibroblast" }, "cellTypeAuthorAnnotation": "NAF_endoneurial, Stroma", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 435.959591, "sdRefIntergenicDistribution": 1.275593, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 2254, "distinctRankCount": 23, "maxRank": 18035.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 176082157, "mappedReadsCount": 121380701, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138899" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000057", "name": "fibroblast" }, "cellTypeAuthorAnnotation": "NAF_perineurial, Stroma", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 80.242157, "sdRefIntergenicDistribution": 1.272718, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 12770, "distinctRankCount": 93, "maxRank": 19156.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 176082157, "mappedReadsCount": 121380701, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138899" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000798", "name": "gamma-delta T cell" }, "cellTypeAuthorAnnotation": "gdT, Immune", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 44.079361, "sdRefIntergenicDistribution": 1.384662, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 23538, "distinctRankCount": 159, "maxRank": 19841.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 176082157, "mappedReadsCount": 121380701, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138899" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000146", "name": "simple columnar epithelial cell" }, "cellTypeAuthorAnnotation": "SMG_Duct, Epithelia", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 11.450908, "sdRefIntergenicDistribution": 1.604917, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 107949, "distinctRankCount": 504, "maxRank": 21593.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 176082157, "mappedReadsCount": 121380701, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138899" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0017000", "name": "pulmonary ionocyte" }, "cellTypeAuthorAnnotation": "Ionocyte_n_Brush, Epithelia", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 113.482456, "sdRefIntergenicDistribution": 1.373069, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 9350, "distinctRankCount": 94, "maxRank": 18877.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 176082157, "mappedReadsCount": 121380701, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138899" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:4033044", "name": "deuterosomal cell" }, "cellTypeAuthorAnnotation": "Deuterosomal, Epithelia", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 79.959541, "sdRefIntergenicDistribution": 1.488119, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 13556, "distinctRankCount": 155, "maxRank": 19372.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 176082157, "mappedReadsCount": 121380701, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138899" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0000319", "name": "mucus secreting cell" }, "cellTypeAuthorAnnotation": "SMG_Mucous, Epithelia", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 35.728339, "sdRefIntergenicDistribution": 1.400868, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 30664, "distinctRankCount": 181, "maxRank": 19885.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 176082157, "mappedReadsCount": 121380701, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138899" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0019001", "name": "tracheobronchial serous cell" }, "cellTypeAuthorAnnotation": "SMG_Serous, Epithelia", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 16.462220, "sdRefIntergenicDistribution": 1.562390, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 69819, "distinctRankCount": 210, "maxRank": 19840.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 176082157, "mappedReadsCount": 121380701, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138899" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0019019", "name": "tracheobronchial smooth muscle cell" }, "cellTypeAuthorAnnotation": "Muscle_smooth_airway, Stroma", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 32.299392, "sdRefIntergenicDistribution": 1.332924, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 32944, "distinctRankCount": 175, "maxRank": 20172.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "single" }, "pipelineSummary": { "allReadsCount": 176082157, "mappedReadsCount": 121380701, "minReadLength": 96, "maxReadLength": 96 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 88396, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Homo", "speciesName": "sapiens", "genomeVersion": "GRCh38.p13", "speciesFullNameWithoutSpace": "Homo_sapiens", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Homo_sapiens/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 9605, "genomeSpeciesId": 9606, "preferredDisplayOrder": 1, "name": "human", "id": 9606 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/", "fileName": "Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ebi.ac.uk/ena/data/view/[experiment_id]", "evidenceUrl": "https://www.ebi.ac.uk/ena/data/view/[evidence_id]", "baseUrl": "https://www.ebi.ac.uk/ena", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 255, "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "id": 103 }, "xRef": { "xRefId": "ERP136992", "xRefName": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "xRefURL": "https://www.ebi.ac.uk/ena/data/view/ERP136992", "source": { "name": "ENA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ebi.ac.uk/ena" } }, "assayCount": 0, "dOI": "10.1038/s41588-022-01243-4", "name": "A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche", "description": "Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).", "id": "ERP136992" }, "id": "ERX9138899" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0003126", "name": "trachea" }, "anatEntityAuthorAnnotation": "Trachea", "cellType": { "id": "CL:0002376", "name": "non-myelinating Schwann cell" }, "cellTypeAuthorAnnotation": "Schwann_nonmyelinating, Stroma", "devStage": { "id": "HsapDv:0000169", "name": "75-year-old stage (human)" }, "devStageAuthorAnnotation": "75-80 (75 in HCA)", "sex": "female", "strain": "White", "time": "NA", "timeUnit": "NA", "species": { "id": 9606, "name": "human", "genus": "Homo", "speciesName": "sapiens", "preferredDisplayOrder": 1 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 198.230175, "sdRefIntergenicDistribution": 1.221333, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 4941, "distinctRankCount": 36, "maxRank": 18655.00 }, "barcode": "" } ], "downloadUrls": [ { "text": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens", "href": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz", "title": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_ERP136992.tsv.gz" }, { "text": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens", "href": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/Homo_sapiens_ERP136992_droplet_based.h5ad", "title": "Homo_sapiens_ERP136992_droplet_based.h5ad" } ] } }